def test_write_hdf5(self, delete=True):
flag = DataQualityFlag(FLAG1, active=ACTIVE, known=KNOWN)
hdfout = self.tmpfile % 'hdf'
try:
flag.write(hdfout)
except ImportError as e:
self.skipTest(str(e))
else:
if delete:
os.remove(hdfout)
return hdfout
def test_write_hdf5(self, delete=True):
flag = DataQualityFlag(FLAG1, active=ACTIVE, known=KNOWN)
hdfout = self.tmpfile % 'hdf'
try:
flag.write(hdfout)
except ImportError as e:
self.skipTest(str(e))
else:
if delete:
os.remove(hdfout)
return hdfout
idxhighscat = argwhere(scatf2>=thresh)
highscatf2 = scatf2[idxhighscat]
highscattimes = times[idxhighscat]
highscattimesgps = highscattimes+start_time
# save text file with values above threshold [GPS f2 index]
outdata = hstack((highscattimesgps,highscatf2,idxhighscat))
savetxt('%s-ALL-TIMES-SCATTER-GT%dHZ-%d-%d.txt' % (ifo,thresh,start_time,dur),outdata,fmt='%f %f %i')
# save segments XML file with segments (based off code from Duncan Macleod)
from math import (floor, ceil)
from gwpy.segments import (Segment, DataQualityFlag)
flag = '%s:DCH-SCATTERED_LIGHT_GT%dHZ:1' % (ifo,thresh)
flag = DataQualityFlag(flag)
segs = []
append = segs.append
for gps in highscattimesgps:
if len(segs) and gps in segs[-1]:
continue
seg = Segment(floor(gps), ceil(gps))
append(seg)
flag.active = segs
flag.known = [Segment(start_time, end_time)]
flag.coalesce()
flag.write('%s-%s_%d-%d-%d.xml.gz' % (flag.ifo, flag.tag.replace('-', '_'), flag.version,start_time, dur))
#EOF
break
f.close()
#construct flag and filename
flag_name = 'H1:UPVh-RND:1' #NEEDS TO BE CHANGED
name = 'segments_UPVh_RND.xml' #NEEDS TO BE CHANGED
try:
knownsegments = numpy.loadtxt('total_UPVh_segs.txt')
except:
print 'No total_UPVh_segs.txt file in current working directory. It should have been produced from last loop.'
#knownsegments = numpy.loadtxt(total_UPVh_segs.txt'
known_start = [knownsegments[i, 0] for i in range(len(knownsegments))]
known_end = [knownsegments[i, 1] for i in range(len(knownsegments))]
# read the data
data = numpy.loadtxt('total_UPVh_trigs.txt', dtype=float)
# get an array for the start_time and end_time of each segment
start_time = [data[i, 0] for i in range(len(data))]
end_time = [data[i, 1] for i in range(len(data))]
# create a data quality flag object
#zip will truncate the start and end time. is this OK?
flag = DataQualityFlag(flag_name,
active=zip(start_time, end_time),
known=zip(known_start, known_end))
# write flag
flag.write(name)
def main(args=None):
"""Run the gwvet-hug CLI tool
"""
parser = create_parser()
args = parser.parse_args(args=args)
# check to make sure we're within the time window of aLIGO,
# and that end_time is after start_time
if args.gpsstart < 971574400: # roughly the end of S6
parser.error("gpsstart before S6")
if args.gpsend < args.gpsstart:
parser.error("end_time is before gpsstart")
# finds beginning of day for given gps time
start_of_day = tconvert(args.gpsstart)
start_of_day_utc = start_of_day.replace(hour=0, minute=0, second=0)
start_of_day_gps = tconvert(start_of_day)
# finds UTC version of start/end times
start_time_utc = tconvert(args.gpsstart)
end_time_utc = tconvert(args.gpsend)
# opens files to be ready for writing
f = open("total_" + args.dq_flag_type + "_trigs.txt", "w") # all triggers
g = open("total_" + args.dq_flag_type + "_segs.txt", "w") # all segments
# choosing to read in hveto
if args.dq_flag_type == 'hveto':
LOGGER.info('Data Quality Flag chosen is hveto, stored in the path '
'%s' % args.directory_path)
# choosing the offline hveto option for O1, runs by Josh Smith
if args.online_offline == 'offline':
analysis_segs_45689 = ['4', '5', '6', '7', '9']
analysis_segs_237 = ['2', '3']
if args.hveto_analysis_seg in analysis_segs_45689:
pattern_trigs_hveto = os.path.join(
args.directory_path,
'analysis%s' % args.hveto_analysis_seg,
'H1-omicron_BOTH-*-DARM',
'*VETO_SEGS_ROUND*.txt',
)
pattern_segs_hveto = os.path.join(
args.directory_path,
'analysis%s' % args.hveto_analysis_seg,
'H1-omicron_BOTH-*-DARM',
'segs.txt',
)
elif args.hveto_analysis_seg in analysis_segs_237:
pattern_trigs_hveto = os.path.join(args.directory_path,
'H1-omicron_BOTH-*-DARM',
'*VETO_SEGS_ROUND*.txt')
pattern_segs_hveto = os.path.join(args.directory_path,
'H1-omicron_BOTH-*-DARM',
'segs.txt')
elif args.hveto_analysis_seg == '8':
pattern_trigs_hveto = os.path.join(args.directory_path,
'*VETO_SEGS_ROUND*.txt')
pattern_segs_hveto = os.path.join(args.directory_path,
'segs.txt')
else:
raise ValueError('Must choose from O1 analysis segments '
'1 through 9')
LOGGER.info(
'Data Quality Flag chosen is hveto, stored in the path '
'%s' % args.directory_path)
while start_time_utc < end_time_utc:
day = start_time_utc.day
month = start_time_utc.month
year = start_time_utc.year
triggers = grab_time_triggers(pattern_trigs_hveto,
args.gpsstart, args.gpsend)
# Ideally we would be able to use the same algorithm, but
# SegmentList.read doesn't support csv, which is the format
# that segment files are recorded in. So, we want to
# temporarily use another method to read in segments.
segments = grab_time_segments(pattern_segs_hveto,
args.gpsstart, g)
start_time_utc += datetime.timedelta(days=1)
write_segs(triggers, f)
elif args.online_offline == 'online':
# These paths are currently hardwired for online searches.
pattern_trigs_hveto = os.path.join(args.directory_path, '{}{:02}',
'{}{:02}{:02}', '*86400-DARM',
'*VETO_SEGS_ROUND*.txt')
pattern_segs_hveto = os.path.join(args.directory_path, '{}{:02}',
'{}{:02}{:02}', '*86400-DARM',
'segs.txt')
triggers = SegmentList([])
segments = SegmentList([])
while start_time_utc < end_time_utc:
day = start_time_utc.day
month = start_time_utc.month
year = start_time_utc.year
wildcard_trigs_hveto = pattern_trigs_hveto.format(
year, month, year, month, day)
wildcard_segs_hveto = pattern_segs_hveto.format(
year, month, year, month, day)
triggers = grab_time_triggers(wildcard_trigs_hveto,
args.gpsstart, args.gpsend)
# Ideally we would be able to use the same algorithm, but
# SegmentList.read doesn't support csv, which is the format
# segment files are recorded in. So, we want to temporarily
# use another method to read segments in.
segments = grab_time_segments(wildcard_segs_hveto,
args.gpsstart, g)
start_time_utc += datetime.timedelta(days=1)
write_segs(triggers, f)
# segments.write(g)
else:
LOGGER.info('Did not choose online or offline. Please choose.')
# choosing to read in UPVh!
elif args.dq_flag_type == 'UPVh':
LOGGER.info('Data-quality flag chosen is %s, stored in the path %s' %
(args.dq_flag_type, args.directory_path))
pattern_trigs_UPVh = os.path.join(args.directory_path,
'DARM_LOCK_{}_{}-H', 'H1:*veto.txt')
pattern_segs_UPVh = os.path.join(args.directory_path,
'DARM_LOCK_{}_{}-H', 'segments.txt')
triggers = SegmentList([])
segments = SegmentList([])
while start_of_day_utc < end_time_utc:
start_of_day_gps = tconvert(start_of_day_utc)
nextday_utc = start_of_day_utc + datetime.timedelta(days=1)
nextday_gps = tconvert(nextday_utc)
wildcard_UPVh_trigs = pattern_trigs_UPVh.format(
start_of_day_gps, nextday_gps)
wildcard_UPVh_segs = pattern_segs_UPVh.format(
start_of_day_gps, nextday_gps)
triggers = grab_time_triggers(wildcard_UPVh_trigs, args.gpsstart,
args.gpsend)
segments = grab_time_triggers(wildcard_UPVh_segs, args.gpsstart,
args.gpsend)
start_of_day_utc += datetime.timedelta(days=1)
write_segs(triggers, f)
write_segs(segments, g)
else: # forgot to choose UPVh or hveto
raise ValueError('Did not give a valid data-quality tool, '
'please choose from hveto, UPVh, or OVL')
f.close()
g.close()
# creating DQ .xml file
# construct flag and filename
flag_name = 'H1:' + args.dq_flag_type + '-RND:1'
name = 'segments_' + args.dq_flag_type + '_RND.xml'
# reading in segment files
try:
knownsegments = numpy.loadtxt('total_' + args.dq_flag_type +
'_segs.txt')
except OSError:
LOGGER.info("No total_{}_segs.txt file in current working directory. "
"It should have been produced from last loop. "
"If this file is empty, that may mean you have no active "
"segments during this time period.".format(
args.dq_flag_type))
known_start = [knownsegments[i, 0] for i in range(len(knownsegments))]
known_end = [knownsegments[i, 1] for i in range(len(knownsegments))]
# reading in trigger files
data = numpy.loadtxt('total_' + args.dq_flag_type + '_trigs.txt')
# get an array for the start_time and end_time of each segment
start_time = [data[i, 1] for i in range(len(data))]
end_time = [data[i, 2] for i in range(len(data))]
# create a data quality flag object
flag = DataQualityFlag(flag_name,
active=zip(start_time, end_time),
known=zip(known_start, known_end))
# write flag
flag.write(name)
LOGGER.info("Created DQ Flag: " + flag_name + " in .xml form as: " + name)
# creating VET .ini file
config = ConfigParser()
config.add_section('plugins')
config.set('plugins', 'gwvet.tabs', ' ')
config.add_section('states')
config.set('states', 'Science', '%(ifo)s:DMT-ANALYSIS_READY:1')
config.add_section('segment-database')
config.set('segment-database', 'url', 'https://segments.ligo.org')
config.add_section('')
config.set('', 'type', 'veto-flag')
config.set('', 'event-channel', '%(ifo)s:GDS-CALIB_STRAIN')
config.set('', 'event-generator', 'Omicron')
config.set(
'', 'metrics', "'Deadtime',\n'Efficiency', \n'Efficiency/Deadtime', "
"\n'Efficiency | SNR>=8', \n'Efficiency/Deadtime | SNR>=8', "
"\n'Efficiency | SNR>=20', \n'Efficiency/Deadtime | SNR>=20', "
"\n'Efficiency | SNR>=100', \n'Efficiency/Deadtime | SNR>=100',"
" \n'Use percentage', \n'Loudest event by SNR'")
config.add_section('tab-SNR-6')
config.set('tab-SNR-6', 'name', 'SNR 6')
config.set('tab-SNR-6', 'type', 'veto-flag')
config.set('tab-SNR-6', 'shortname', 'SNR 6')
config.set('tab-SNR-6', 'flags', flag_name)
config.set('tab-SNR-6', 'states', "Science")
config.set('tab-SNR-6', 'segmentfile', name)
with open(args.dq_flag_type + '_segs.ini', 'wb') as configfile:
config.write(configfile)
LOGGER.info(
'\n Created %s_segs.ini. You have everything you need to run VET now! '
'\n' % args.dq_flag_type)
LOGGER.info(
'To run VET,first go into %s_segs.ini, and delete the line that only '
'contains [], then save and exit the .ini file.\n' % args.dq_flag_type)
LOGGER.info(
'Finally, run the command: \n'
'$ gw_summary gps %s %s -f /home/detchar/etc/summary/configurations/'
'defaults.ini -f %s_segs.ini' %
(args.gpsstart, args.gpsend, args.dq_flag_type))
# name the DQ flag
optic = channel[0].split('_')[2]
flag_name = 'L1:DCH-EQ_%s_GT_%s:1' % (optic, thresh)
# grab all observing (or whatever is defined) time
active = DataQualityFlag.query_dqsegdb(args.science, args.start, args.end).active
# grab only data for the STS channel in observing time
data = get_timeseries_dict(channel, active, frametype='L1_M')
# find times above threshold
time = [j.times[j > thresh] for j in data[channel[0]]]
times = numpy.concatenate(time)
# put all times above threshold in to segments
segs = segments.segmentlist()
segs.extend([segments.segment(int(t.value), int(t.value)+args.stride) for t in times])
segs = segs.coalesce()
# set up the xml file by making a list of the start and end times of the flag
start_time = []
start_time.extend([t[0] for t in segs])
end_time = []
end_time.extend([t[1] for t in segs])
# put in to dq flag object
flag = DataQualityFlag(flag_name, active=zip(start_time,end_time), known=[[args.start,args.end]])
# write flag to xml
flag.write(segment_file)
else:
print filename + " does not exist. Looking for the segment file in next time increment."
break
f.close()
#construct flag and filename
flag_name = 'H1:UPVh-RND:1' #NEEDS TO BE CHANGED
name = 'segments_UPVh_RND.xml' #NEEDS TO BE CHANGED
try: knownsegments = numpy.loadtxt('total_UPVh_segs.txt')
except:
print 'No total_UPVh_segs.txt file in current working directory. It should have been produced from last loop.'
#knownsegments = numpy.loadtxt(total_UPVh_segs.txt'
known_start = [knownsegments[i,0] for i in range(len(knownsegments))]
known_end = [knownsegments[i,1] for i in range(len(knownsegments))]
# read the data
data = numpy.loadtxt('total_UPVh_trigs.txt', dtype=float)
# get an array for the start_time and end_time of each segment
start_time = [data[i,0] for i in range(len(data))]
end_time = [data[i,1] for i in range(len(data))]
# create a data quality flag object
#zip will truncate the start and end time. is this OK?
flag = DataQualityFlag(flag_name, active=zip(start_time, end_time), known=zip(known_start, known_end))
# write flag
flag.write(name)
def mkSegment(gst, get, utc_date, txt=True):
for key in keys:
sources = GetFilelist(gst, get, key)
first = True
for source in sources:
events = EventTable.read(
source,
tablename='sngl_burst',
columns=['start_time', 'start_time_ns', 'duration', 'snr'])
#events = EventTable.read(source, tablename='sngl_burst',columns=['peak_time', 'peak_time_ns','start_time', 'start_time_ns', 'duration', 'peak_frequency', 'central_freq', 'bandwidth', 'channel', 'amplitude', 'snr', 'confidence', 'chisq', 'chisq_dof', 'param_one_name', 'param_one_value'])
col = events.get_column('start_time')
if first:
if len(col) > 0:
mergedevents = events
first = False
else:
pass
else:
mergedevents = vstack([mergedevents, events])
for snr in snrs[key]:
Triggered = DataQualityFlag(name="K1:" + key,
known=[(gst, get)],
active=[],
label="Glitch",
description="Glitch veto segment K1:" +
key + " >= SNR" + str(snr))
#Triggered.ifo = "K1"
if not first:
fevents = mergedevents.filter(
('snr', mylib.Islargerequal, snr))
durations = fevents.get_column('duration')
start_times = fevents.get_column('start_time')
for start_time, duration in zip(start_times, durations):
tmpstart = int(start_time)
#tmpend = start_time + duration
tmpend = int(start_time + 1)
tmpsegment = Segment(tmpstart, tmpend)
tmpTriggered = DataQualityFlag(known=[(gst, get)],
active=[(tmpstart, tmpend)])
Triggered |= tmpTriggered
#dqflag['K1-GRD_SCIENCE_MODE'].description = "Observation mode. K1:GRD-IFO_STATE_N == 1000"
#dqflag['K1-GRD_LOCKED'].name = "K1:GRD-LSC_LOCK_STATE_N >= 300 & K1:GRD-LSC_LOCK_STATE_N <= 1000"
# write down 15 min segments.
if txt:
with open(filepath_txt[key + str(snr)], mode='w') as f:
for seg in Triggered.active:
f.write('{0} {1}\n'.format(int(seg[0]), int(seg[1])))
# if accumulated file exists, it is added.
if os.path.exists(filepath_xml[key + str(snr)]):
tmp = DataQualityFlag.read(filepath_xml[key + str(snr)])
Triggered = Triggered + tmp
Triggered.write(filepath_xml[key + str(snr)], overwrite=True)
start_time_nss = fevents.get_column('start_time_ns')
# col can be used like array. col[0] will give first value.
for peak_time,peak_time_ns,duration,start_time,start_time_ns in zip(peak_times,peak_time_nss,durations,start_times,start_time_nss):
#tmpstart=start_time-tfile
tmpstart=start_time
tmpstart+=start_time_ns*1e-9
tmpend=tmpstart+duration
tmpstart=round(tmpstart,4)
tmpend=round(tmpend,4)
tmpTriggered = DataQualityFlag(known=[(gpsstart,gpsend)],active=[(tmpstart,tmpend)])
Triggered |= tmpTriggered
#if kamioka:
# fname='/users/.ckozakai/KashiwaAnalysis/analysis/code/gwpy/trigger/triggerStudy/condor/'+date+'/segment/'+date+'_segment_SNR' + str(SNR) + '_' + channel + '_' + str(tfile) +'_60.xml'
#else:
# fname='/home/chihiro.kozakai/detchar/analysis/code/gwpy/trigger/triggerStudy/condor/'+date+'/segment/'+date+'_segment_SNR' + str(SNR) + '_' + channel + '_' + str(tfile) +'_60.xml'
#Triggered.write(fname,overwrite=True)
Triggered.write(outfile,overwrite=True)
print(Triggered)
txt = outfile.replace('.xml','.txt')
with open(txt, mode='w') as f:
for seg in Triggered.active :
#f.write('{0} {1}\n'.format(int(seg[0]), int(seg[1])))
f.write('{0} {1}\n'.format(seg[0], seg[1]))
