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preprocess.py
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preprocess.py
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import logging,logging.handlers,datetime,math,sys,socket,os,json,shutil,io,re
from optparse import OptionParser,OptionGroup
import threading
import urllib2, urllib
import base64
import time
import subprocess
import ssl
import uuid
import stat
from astropy.table import Table,Column
from astropy.time import Time
from astropy.coordinates import SkyCoord
import collections
if sys.version_info[0] >= 3:
from http.client import HTTPSConnection
else:
from httplib import HTTPSConnection
import extra_utils
logger=extra_utils.makelogger('preprocess')
import mwapy
from mwapy import metadata
import find_calibrator
################################################################################
# from obsdownload.py
# 2016-08-17
################################################################################
KEY_FILE = os.path.join(os.getenv('HOME'),'obskey.key')
CERT_FILE = os.path.join(os.getenv('HOME'),'obscrt.crt')
######################################################################
class HTTPSClientAuthConnection(HTTPSConnection):
"""Class to make a HTTPS connection, with support for full client-based SSL Authentication"""
def __init__(self, host, key_file, cert_file, timeout=None):
HTTPSConnection.__init__(self, host, key_file=key_file, cert_file=cert_file)
self.key_file = key_file
self.cert_file = cert_file
self.ca_file = None
self.timeout = timeout
def connect(self):
""" Connect to a host on a given (SSL) port.
If ca_file is pointing somewhere, use it to check Server Certificate.
Redefined/copied and extended from httplib.py:1105 (Python 2.6.x).
This is needed to pass cert_reqs=ssl.CERT_REQUIRED as parameter to ssl.wrap_socket(),
which forces SSL to check server certificate against our client certificate.
"""
sock = socket.create_connection((self.host, self.port), self.timeout)
if self._tunnel_host:
self.sock = sock
self._tunnel()
# If there's no CA File, don't force Server Certificate Check
if self.ca_file:
self.sock = ssl.wrap_socket(sock, self.key_file, self.cert_file,
ca_certs=self.ca_file, cert_reqs=ssl.CERT_REQUIRED)
else:
self.sock = ssl.wrap_socket(sock, self.key_file, self.cert_file, cert_reqs=ssl.CERT_NONE)
class FileStatus():
def __init__(self, numfiles):
self.status = {}
self.lock = threading.RLock()
self.errors = []
self.filesComplete = 0
self.totalfiles = numfiles;
def file_error(self, err):
with self.lock:
self.errors.append(err)
print(err)
def file_starting(self, filename):
with self.lock:
print('%s [INFO] Downloading %s' % (time.strftime('%c'), filename))
def file_complete(self, filename):
with self.lock:
self.filesComplete = self.filesComplete + 1
print('%s [INFO] %s complete [%d of %d]' % (time.strftime('%c'), filename,
self.filesComplete, self.totalfiles))
# def delete_key_file():
# try:
# os.remove(KEY_FILE)
# except:
# pass
# try:
# os.remove(CERT_FILE)
# except:
# pass
# def create_key_file():
# tmpkey = str(uuid.uuid1())
# tmpcert = str(uuid.uuid1())
# with open(tmpkey, 'wb') as out:
# out.write(KEY)
# out.flush()
# with open(tmpcert, 'wb') as out:
# out.write(CERT)
# out.flush()
# os.rename(tmpkey, KEY_FILE)
# os.rename(tmpcert, CERT_FILE)
# os.chmod(KEY_FILE, stat.S_IRUSR)
# os.chmod(CERT_FILE, stat.S_IRUSR)
######################################################################
def query_observation(obs=None, host=None, flagonly=False, metaonly=False, uvfits=False, chstart=None, chcount=False):
if not os.path.exists(KEY_FILE):
logger.error('Unable to find HTTPS key file %s' % KEY_FILE)
return None
if not os.path.exists(CERT_FILE):
logger.error('Unable to find HTTPS certificate file %s' % CERT_FILE)
return None
response = None
try:
conn = HTTPSClientAuthConnection(host, key_file=KEY_FILE, cert_file=CERT_FILE)
conn.request('GET', '/QUERY?query=files_like&like=%s%%&format=json' % obs)
response = conn.getresponse()
if response.status != 200:
raise Exception('HTTP error: %s Reason: %s' \
% (response.status, response.reason))
length = int(response.getheader('content-length', 0))
buffsize = 4096
readin = 0
resultbuffer = []
while readin < length:
left = length - readin
buff = response.read(buffsize if left >= buffsize else left)
if not buff:
raise Exception('socket read error')
resultbuffer.append(buff)
readin += len(buff)
filemap = {}
json_files = json.loads(b''.join(resultbuffer).decode('utf8'))
files = json_files.get('files_like', [])
for f in files:
add = False
filename = f['col3']
filesize = f['col6']
if flagonly or uvfits or metaonly:
if 'flags.zip' in filename and flagonly:
add = True
if '.uvfits' in filename and uvfits:
add = True
if '_ppds' in filename and metaonly:
add = True
else:
if chstart is not None:
# it must be a valid MWA visibility fits file which contains
# the coarse channel. If valid extract the coarse channel
# and check with the range requested.
try:
num = int(filename.split('_')[2].split('gpubox')[1])
if (num >= chstart) and (num < chstart+chcount):
add = True
except:
pass
else:
add = True
if add is True:
filemap[filename] = filesize
return filemap
finally:
if response:
response.close()
######################################################################
def check_complete(filename, size, dir):
path = dir + filename
if os.path.isfile(path) is True:
filesize = os.stat(path).st_size
if filesize == int(size):
return True
return False
######################################################################
def download_worker(url, host, size, filename, sem, out, stat, bufsize):
resp = None
try:
stat.file_starting(filename)
conn = HTTPSClientAuthConnection(host, key_file = KEY_FILE,
cert_file = CERT_FILE, timeout = 5000)
conn.request('GET', '/RETRIEVE?file_id=%s' % filename)
response = conn.getresponse()
if response.status != 200:
raise Exception('HTTP error: %s Reason: %s' \
% (response.status, response.reason))
length = int(response.getheader('content-length', 0))
with open(out + filename, 'wb') as f:
readin = 0
while readin < length:
try:
response.fp._sock.settimeout(120)
except:
pass
left = length - readin
buff = response.read(bufsize if left >= bufsize else left)
if not buff:
raise Exception('socket read error')
f.write(buff)
readin += len(buff)
stat.file_complete(filename)
except Exception as exp:
stat.file_error('%s [ERROR] %s: %s' % (time.strftime('%c'), filename,
str(exp)))
finally:
if resp:
resp.close()
sem.release()
######################################################################
def run_obsdownload(obs,ngashost='fe1.pawsey.org.au:8777',
numdownload=4):
try:
# get system TCP buffer size
s = socket.socket(socket.AF_INET, socket.SOCK_STREAM)
bufsize = s.getsockopt(socket.SOL_SOCKET, socket.SO_RCVBUF)
s.close()
if numdownload <= 0 or numdownload > 6:
logger.error('Number of simultaneous downloads must be > 0 and <= 6')
return None
logger.info('Finding observation %s' % (obs,))
fileresult = query_observation(obs, ngashost)
if len(fileresult) <= 0:
logger.error('No file(s) found for observation %s' % (obs,))
return None
logger.info('Found %s files' % (str(len(fileresult)),))
outputdir=os.path.join(os.curdir,
str(obs),'')
if not os.path.exists(outputdir):
os.makedirs(outputdir)
urls = []
stat = FileStatus(len(fileresult))
for key, value in fileresult.items():
url = 'https://%s/RETRIEVE?file_id=%s' % (ngashost, key)
if check_complete(key, int(value), outputdir) is False:
urls.append((url, value, key))
else:
stat.file_complete(key)
threads = []
sem = threading.BoundedSemaphore(value = numdownload)
for u in urls:
while True:
if sem.acquire(blocking = False):
t = threading.Thread(target = download_worker,
args = (u[0], ngashost, u[1], u[2],
sem, outputdir, stat, int(bufsize)))
t.setDaemon(True)
t.start()
threads.append(t)
break
else:
time.sleep(1)
# wait for all the threads to finish
while len(threads) > 0:
for t in list(threads):
t.join(1)
if not t.isAlive():
threads.remove(t)
logger.info('File Transfer Complete.')
# check if we have errors
if stat.errors:
logger.warning('File Transfer Error Summary:')
for errs in stat.errors:
logger.warning(errs)
raise Exception()
else:
logger.info('File Transfer Success.')
return fileresult
except KeyboardInterrupt as k:
logger.error('Interrupted; terminating download')
return None
except Exception as e:
logger.error(e)
return None
################################################################################
# from obsdownload.py
# 2015-02-05
################################################################################
# username = 'ngas'
# password = base64.decodestring('bmdhcw==')
# ######################################################################
# class PrintStatus():
# def __init__(self, numfiles):
# self.status = {}
# self.lock = threading.RLock()
# self.currentbytes = 0
# self.totalbytes = 0
# self.runtime = 0
# self.errors = []
# self.files = 0
# self.filesComplete = 0
# self.totalfiles = numfiles;
# def fileError(self, err):
# with self.lock:
# self.errors.append(err)
# logger.error(err)
# def fileStarting(self, filename):
# with self.lock:
# logger.info('Downloading %s' % (filename))
# def fileComplete(self, filename):
# with self.lock:
# self.filesComplete = self.filesComplete + 1
# logger.info('%s complete [%d of %d]' % (filename,
# self.filesComplete,
# self.totalfiles))
# ######################################################################
# def queryObs(obs, host, flagonly):
# #http://fe1.pawsey.ivec.org:7777/QUERY?query=files_like&like=1061316296%&format=json
# base64string = base64.encodestring('%s:%s' % (username, password)).replace('\n', '')
# url = 'http://%s/QUERY?' % host
# data = "query=files_like&like=" + str(obs) + "%&format=json"
# response = None
# try:
# # Send HTTP POST request
# request = urllib2.Request(url + data)
# request.add_header("Authorization", "Basic %s" % base64string)
# response = urllib2.urlopen(request)
# resultbuffer = ''
# while True:
# result = response.read(2048)
# if result:
# resultbuffer = resultbuffer + result
# else:
# break
# filemap = {}
# files = json.loads(resultbuffer)['files_like']
# for f in files:
# # retrieve flag files only
# if flagonly:
# if 'flags.zip' in f['col3']:
# filemap[f['col3']] = f['col6']
# # else add all the files: having a map removes diplicates
# else:
# filemap[f['col3']] = f['col6']
# return filemap
# finally:
# if response:
# response.close()
# ######################################################################
# def checkFile(filename, size, dir):
# path = dir + filename
# # check the file exists
# if os.path.isfile(path) is True:
# #check the filesize matches
# filesize = os.stat(path).st_size
# if filesize == int(size):
# return True
# return False
# ######################################################################
# def worker(url, size, filename, s, out, stat, bufsize):
# u = None
# f = None
# try:
# stat.fileStarting(filename)
# # open file URL
# request = urllib2.Request(url)
# base64string = base64.encodestring('%s:%s' % (username, password)).replace('\n', '')
# request.add_header("Authorization", "Basic %s" % base64string)
# u = urllib2.urlopen(request, timeout=1400)
# u.fp.bufsize = bufsize
# # get file size
# meta = u.info()
# file_size = int(meta.getheaders("Content-Length")[0])
# # open file for writing
# f = open(out + filename, 'wb')
# current = 0
# file_size_dl = 0
# block_sz = bufsize
# while file_size_dl < file_size:
# buffer = u.read(block_sz)
# if buffer:
# f.write(buffer)
# current = len(buffer)
# file_size_dl += current
# else:
# if file_size_dl != file_size:
# raise Exception("size mismatch %s %s" % str(file_size), str(file_size_dl))
# break
# stat.fileComplete(filename)
# except urllib2.HTTPError as e:
# stat.fileError("%s [ERROR] %s %s" % (time.strftime("%c"), filename, str(e.read()) ))
# except urllib2.URLError as urlerror:
# if hasattr(urlerror, 'reason'):
# stat.fileError("%s [ERROR] %s %s" % (time.strftime("%c"), filename, str(urlerror.reason) ))
# else:
# stat.fileError("%s [ERROR] %s %s" % (time.strftime("%c"), filename, str(urlerror) ))
# except Exception as exp:
# stat.fileError("%s [ERROR] %s %s" % (time.strftime("%c"), filename, str(exp) ))
# finally:
# if u != None:
# u.close()
# if f != None:
# f.flush()
# f.close()
# s.release()
# ######################################################################
# def old.run_obsdownload(obs,ngashost='fe1.pawsey.ivec.org:7777',
# numdownload=4):
# if numdownload <= 0 or numdownload>6:
# logger.error('Number of downloads must be between 0 and 6')
# return None
# try:
# # get system TCP buffer size
# s = socket.socket(socket.AF_INET, socket.SOCK_STREAM)
# bufsize = s.getsockopt(socket.SOL_SOCKET, socket.SO_RCVBUF)
# s.close()
# logger.info('Finding observation %s' % obs)
# fileresult = queryObs(obs, ngashost, False)
# #fileresult = queryObs(obs, ngashost, True)
# if len(fileresult) <= 0:
# logger.error('No files found for observation %s' % obs)
# return None
# logger.info('Found %s files' % len(fileresult))
# outputdir=os.path.join(os.curdir,
# str(obs),
# '')
# if not os.path.exists(outputdir):
# os.makedirs(outputdir)
# stat = PrintStatus(len(fileresult))
# urls = []
# for key, value in fileresult.iteritems():
# url = "http://" + ngashost + "/RETRIEVE?file_id=" + key
# if checkFile(key, int(value), outputdir) is False:
# urls.append((url, value, key))
# # stat.update(url, r[2], 0, 0, 0, 0)
# else:
# stat.fileComplete(key)
# s = threading.BoundedSemaphore(value=numdownload)
# for u in urls:
# while(1):
# if s.acquire(blocking=False):
# t = threading.Thread(target=worker, args=(u[0],u[1],u[2],s,outputdir,stat,int(bufsize)))
# t.setDaemon(True)
# t.start()
# break
# else:
# time.sleep(1)
# while (1):
# main_thread = threading.currentThread()
# # if the main thread and print thread are left then we must be done; else wait join
# if len(threading.enumerate()) == 1:
# break;
# for t in threading.enumerate():
# # if t is main_thread or t is status_thread:
# if t is main_thread:
# continue
# t.join(1)
# if t.isAlive():
# continue
# logger.info('File Transfer Complete')
# # check if we have errors
# if len(stat.errors) > 0:
# logger.warning('File Transfer Error Summary:')
# for i in stat.errors:
# logger.warning(i)
# #raise Exception()
# else:
# logger.info('File Transfer Success')
# return fileresult
# except KeyboardInterrupt as k:
# logger.error('Interrupted; terminating download')
# return None
# except Exception as e:
# logger.error(e)
# return None
##################################################
def tokenize(input):
"""
web queries use different wildcards than normal people
turn ? to _
turn % to *
"""
if input is not None:
input=input.replace('_','\_')
return input.replace('?','_').replace('*','%')
else:
return input
##################################################
def parse_time(input):
"""
parse input time (GPStime or datetime string)
"""
try:
return int(input)
except ValueError:
# try to parse it as a date
try:
t=Time(input, scale='utc')
except ValueError,e:
try:
t=Time(datetime.datetime.strptime(input, '%Y%m%d%H%M%S'), scale='utc')
except ValueError,e:
logger.error('Unable to parse input time %s: %s' % (input,
e))
return None
return int(t.gps)
######################################################################
def get_size(start_path = '.'):
total_size = 0
for dirpath, dirnames, filenames in os.walk(start_path):
for f in filenames:
fp = os.path.join(dirpath, f)
total_size += os.path.getsize(fp)
return total_size
######################################################################
def get_free(path=None):
if path is None:
path=os.path.abspath(os.cwd())
if ':' in path:
# assume a remote location
# need ssh
host,path=path.split(':')
command='ssh %s "df -k %s"' % (host,path)
try:
result=subprocess.check_output(command, shell=True)
if len(result.split('\n'))==3:
return int(result.split('\n')[1].split()[3])*1024
elif len(result.split('\n'))==4:
print result.split('\n')[2]
# an extra line-break
return int(result.split('\n')[2].split()[2])*1024
except Exception, e:
logger.error('Unable to check free space on %s:%s\n%s' % (host,path,e))
return 0
else:
# it is local
try:
stat=os.statvfs(path)
except OSError:
return 0
return stat.f_bavail*stat.f_bsize
######################################################################
class Observation():
##############################
def __init__(self, obsid, basedir='./', clobber=False,
cleanfits=False,
cleanms=False,
cleanflag=False,
checkfree=True,
checksize=True,
copycommand='rsync -aruvP'):
self.obsid=obsid
self.basedir=basedir
self.downloadedfiles=None
self.metafits=None
self.cottercommand=None
self.msfile=None
self.clobber=clobber
self.copycommand=copycommand
self.cleanfits=cleanfits
self.cleanms=cleanms
self.cleanflag=cleanflag
self.destination=None
self.rawsize=None
self.fitssize=None
self.mssize=None
self.checkfree=checkfree
self.checksize=checksize
self.outputdir=os.path.join(self.basedir,
str(self.obsid),
'')
os.chdir(basedir)
logger.info('##################################################')
logger.info('%d' % self.obsid)
self.observation=metadata.MWA_Observation(self.obsid)
logger.debug('\n' + str(self.observation))
obsinfo=metadata.fetch_obsinfo(self.obsid)
self.rawsize=sum([obsinfo['files'][f]['size'] for f in obsinfo['files'].keys()])
self.fitssize=sum([obsinfo['files'][f]['size']*(obsinfo['files'][f]['filetype']==8) for f in obsinfo['files'].keys()])
logger.info('Raw data size is %.1f MB' % (self.rawsize/1024./1024.))
##############################
def __del__(self):
if self.cleanfits:
logger.warning('Deleting downloaded FITS files %s' % ','.join(self.downloadedfiles))
for f in self.downloadedfiles:
os.remove(os.path.join(self.outputdir,f))
if self.cleanms:
if self.destination is None:
logger.warning('Requesting delete of MS file %s, but it has not been copied elsewhere' % self.msfile)
else:
logger.warning('Deleting MS file %s' % self.msfile)
shutil.rmtree(os.path.join(self.outputdir,self.msfile))
if self.cleanflag:
logger.warning('Deleting downloaded flag files %s/*.mwaf' % self.outputdir)
for f in glob.glob('%s/*.mwaf' % self.outputdir):
os.remove(f)
##############################
def download(self, numdownload=4):
if self.checkfree and (self.rawsize is not None and self.rawsize > 0 and self.rawsize > get_free(self.basedir)):
logger.error('Data download will require %.1f MB, but only %.1f MB free space on %s' % (self.rawsize/1024./1024,
get_free(self.basedir)/1024./1024,
self.basedir))
return None
self.downloadedfiles=run_obsdownload(self.obsid, numdownload=numdownload)
#downloadedfiles2=run_obsdownload(self.obsid, numdownload=numdownload)
#for k in downloadedfiles2.keys():
# self.downloadedfiles[k]=downloadedfiles2[k]
os.system(s)
return self.downloadedfiles
##############################
def makemetafits(self, min_bad_dipoles=5):
logger.info('Making metafits with min_bad_dipoles=%d' % min_bad_dipoles)
m=metadata.instrument_configuration(self.obsid, min_bad_dipoles=min_bad_dipoles)
h=m.make_metafits()
self.metafits=os.path.join(self.outputdir,'%s.metafits' % self.obsid)
if os.path.exists(self.metafits):
os.remove(self.metafits)
try:
h.writeto(self.metafits)
logger.info('Metafits written to %s' % (self.metafits))
return True
except Exception, e:
logger.error('Unable to write metafits file %s:\n%s' % (self.metafits,e))
return None
##############################
def cotter(self, cottercpus=4,
timeres=4,
freqres=40,
phasecenter=None,
allowmissing=True):
if timeres < self.observation.inttime:
logger.warning('Desired time resolution %.1f s is < native time resolution %.1f s' % (
timeres,self.observation.inttime))
timeres=self.observation.inttime
logger.warning('Changing to %.1f s' % timeres)
if freqres < self.observation.fine_channel:
logger.error('Desired frequency resolution %d kHz is < native frequency resolution %d kHz' % (
freqres,self.observation.fine_channel))
return None
compressionfactor_time=int(timeres/self.observation.inttime)
compressionfactor_freq=int(freqres/self.observation.fine_channel)
logger.info('Expect compression of %d in time and %d in frequency' % (compressionfactor_time,
compressionfactor_freq))
self.mssize=self.fitssize/compressionfactor_time/compressionfactor_freq
if self.checkfree and (self.mssize is not None and self.mssize > 0 and self.mssize > get_free(self.basedir)):
logger.error('Cotter will require %.1f MB, but only %.1f MB free space on %s' % (self.mssize/1024./1024,
get_free(self.basedir)/1024./1024,
self.basedir))
return None
os.chdir(self.outputdir)
self.useflagfiles=False
# check to see if a .zip file for flags was included
for f in self.downloadedfiles:
if '.zip' in f:
logger.info('Unzipping flags from %s' % f)
subprocess.Popen(['unzip','-j',f],stderr=subprocess.PIPE,
stdout=subprocess.PIPE)
self.useflagfiles=True
# cotter gets angry if only one timeslice
newfiles=[]
for f in self.downloadedfiles:
if re.match('\d+_\d+_gpubox\d\d\.fits',f) is not None:
logger.warning('Format for %s is wrong; linking %s_00.fits to %s...' % (f,os.path.splitext(f)[0],f))
try:
os.symlink(f,'%s_00.fits' % os.path.splitext(f)[0])
except OSError:
logger.warning('%s_00.fits exists' % os.path.splitext(f)[0])
newfiles.append('%s_00.fits' % os.path.splitext(f)[0])
for f in newfiles:
self.downloadedfiles[f]=0
self.cottercommand=['cotter','-j',str(cottercpus),
'-m',self.metafits,
'-timeres',str(timeres),
'-freqres',str(freqres),
'-o','%s.ms' % self.obsid]
if self.useflagfiles:
self.cottercommand+=['-flagfiles','%s_%%%%.mwaf' % self.obsid]
#self.cottercommand+=['-norfi']
if phasecenter is not None:
self.cottercommand+=['-centre',phasecenter.to_string('hmsdms').split()[0],
phasecenter.to_string('hmsdms').split()[1]]
if allowmissing:
self.cottercommand+=['-allowmissing']
self.cottercommand+=['*gpubox*_*.fits']
self.msfile='%s.ms' % self.obsid
if os.path.exists(self.msfile):
if not self.clobber:
logger.warning('MSfile %s exists; will not clobber' % self.msfile)
return True
else:
logger.warning('MSfile %s exists; will clobber' % self.msfile)
shutil.rmtree(self.msfile)
logger.info('Will run:\n\t%s' % ' '.join(self.cottercommand))
p=subprocess.Popen(' '.join(self.cottercommand),
stderr=subprocess.PIPE,
stdout=subprocess.PIPE,
shell=True,
close_fds=False)
waserror=False
while True:
p.stdout.flush()
p.stderr.flush()
for l in p.stdout.readlines():
logger.debug(l.rstrip())
for l in p.stderr.readlines():
logger.error(l.rstrip())
waserror=True
returncode=p.poll()
if returncode is not None:
break
time.sleep(1)
if waserror:
logger.error('Cotter had an error')
return None
if not os.path.exists(self.msfile):
logger.error('MSfile %s was not created' % self.msfile)
return None
newsize=get_size(self.msfile)
if math.fabs(newsize-self.mssize)/float(self.mssize) > 0.75 and self.checksize:
logger.error('Expected a size of %d bytes for MSfile %s, but actual file has %d bytes' % (self.mssize,
self.msfile,
newsize))
return None
self.mssize=get_size(self.msfile)
logger.info('MSfile %s was created with size %d bytes' % (self.msfile,self.mssize))
return self.mssize
##############################
def copy(self, destination):
if destination is not None:
if self.checkfree and (self.mssize is not None and self.mssize > 0 and self.mssize > get_free(destination)):
logger.error('Copy will require %.1f MB, but only %.1f MB free space on %s' % (self.mssize/1024./1024,
get_free(destination)/1024./1024,
destination))
return None
copycommand=[self.copycommand,
self.msfile,
destination + '/']
logger.info('Will run:\n\t%s' % ' '.join(copycommand))
p=subprocess.Popen(' '.join(copycommand),
stderr=subprocess.PIPE,
stdout=subprocess.PIPE,
shell=True,
close_fds=False)
while True:
p.stdout.flush()
p.stderr.flush()
for l in p.stdout.readlines():
logger.debug(l.rstrip())
for l in p.stderr.readlines():
logger.error(l.rstrip())
returncode=p.poll()
if returncode is not None:
break
time.sleep(1)
if returncode > 0:
logger.error('Error copying %s to %s' % (self.msfile, destination))
return None
logger.info('%s copied to %s' % (self.msfile,destination))
copycommand=[self.copycommand,
self.metafits,
destination + '/']
logger.info('Will run:\n\t%s' % ' '.join(copycommand))
p=subprocess.Popen(' '.join(copycommand),
stderr=subprocess.PIPE,
stdout=subprocess.PIPE,
shell=True,
close_fds=False)
while True:
p.stdout.flush()
p.stderr.flush()
for l in p.stdout.readlines():
logger.debug(l.rstrip())
for l in p.stderr.readlines():
logger.error(l.rstrip())
returncode=p.poll()
if returncode is not None:
break
time.sleep(1)
if returncode > 0:
logger.error('Error copying %s to %s' % (self.metafits, destination))
return None
logger.info('%s copied to %s' % (self.metafits,destination))
self.destination=destination
return True
######################################################################
def main():
observation_num=None
usage="Usage: %prog [options] <obsids>\n"
parser = OptionParser(usage=usage)
parser.add_option('--start',dest='starttime',default=None,type='str',
help='Starting time for processing (GPSseconds or ISO UT date)')
parser.add_option('--stop',dest='stoptime',default=None,type='str',
help='Final time for processing (GPSseconds or ISO UT date)')
parser.add_option('--proj',dest='project',default=None,
help='Project ID')
parser.add_option('--destination',dest='destination',default=None,
help='Final destination to (remote) copy the MS file')
parser.add_option('--summaryname',dest='summaryname',default=None,
help='Name for output summary table')
parser.add_option('--downloads',dest='downloads',default=4,type='int',
help='Number of simultaneous NGAS downloads [default=%default]')
parser.add_option('--nomissing',dest='allowmissing',default=True,
action='store_false',
help='Do not allow missing GPU box files')
parser.add_option('--timeres',dest='timeres',default=4,type='float',
help='Output time resolution (s) [default=%default]')
parser.add_option('--freqres',dest='freqres',default=40,type='int',
help='Output frequency resolution (kHz) [default=%default]')
parser.add_option('--caltimeres',dest='caltimeres',default=0,type='float',
help='Output time resolution for calibrators (s) [default=<timeres>]')
parser.add_option('--calfreqres',dest='calfreqres',default=0,type='int',
help='Output frequency resolution (kHz) [default=<freqres>]')
parser.add_option('--ra',dest='ra',default=None,
help='Output RA phase center (deg) [default=metafits]')
parser.add_option('--dec',dest='dec',default=None,
help='Output Dec phase center (deg) [default=metafits]')
parser.add_option('--baddipoles',dest='minbaddipoles',default=2,type='int',
help='Number of bad dipoles above which tile is flagged [default=%default]')
parser.add_option('--cal',dest='cal',default=False,
action='store_true',
help='Always include a calibrator observation?')
parser.add_option('--cpus',dest='cottercpus',default=4,type='int',
help='Number of CPUs for cotter [default %default]')
parser.add_option('--clobber',dest='clobber',default=False,action='store_true',
help='Clobber existing MS file? [default=False]')
parser.add_option('--cleanall',dest='cleanall',default=False,action='store_true',
help='Delete downloaded FITS files, flag files, and original MS file when done? [default=False]')
parser.add_option('--cleanfits',dest='cleanfits',default=False,action='store_true',
help='Delete downloaded FITS files when done? [default=False]')
parser.add_option('--cleanms',dest='cleanms',default=False,action='store_true',
help='Delete original MS file when done? [default=False]')
parser.add_option('--copycommand',dest='copycommand',default='rsync -aruvP',
help='Command for (remote) copying [default=%default]')
parser.add_option('--summaryformat',dest='summaryformat',default='ascii.commented_header',
help='Format for output summary table (from astropy.table) [default=%default]')
parser.add_option('--email',dest='notifyemail', default=None,
help='Notification email [default=no email]')
parser.add_option('--ignorespace',dest='ignorespace',default=False,
action='store_true',
help='Ignore free-space for file download, processing, and copying?')
parser.add_option('--ignoresize',dest='ignoresize',default=False,
action='store_true',
help='Ignore size of the .ms file?')
parser.add_option("-v", "--verbose", dest="loudness", default=0, action="count",
help="Each -v option produces more informational/debugging output")
parser.add_option("-q", "--quiet", dest="quietness", default=0, action="count",
help="Each -q option produces less error/warning/informational output")
(options, args) = parser.parse_args()
if options.cleanall:
options.cleanfits=True
options.cleanms=True
options.cleanflag=True
loglevels = {0: [logging.DEBUG, 'DEBUG'],
1: [logging.INFO, 'INFO'],
2: [logging.WARNING, 'WARNING'],
3: [logging.ERROR, 'ERROR'],
4: [logging.CRITICAL, 'CRITICAL']}
logdefault = 2 # WARNING
level = max(min(logdefault - options.loudness + options.quietness,4),0)
logging.getLogger('').handlers[1].setLevel(loglevels[level][0])