lalinference_pipe_utils.py 107 KB
Newer Older
1

2
#flow DAG Class definitions for LALInference Pipeline
3
# (C) 2012 John Veitch, Vivien Raymond, Kiersten Ruisard, Kan Wang
4

John Douglas Veitch's avatar
John Douglas Veitch committed
5
import itertools
6
import glue
7
from glue import pipeline,segmentsUtils,segments
8
import os
9
import socket
10
from lalapps import inspiralutils
11 12
import uuid
import ast
13
import pdb
John Douglas Veitch's avatar
John Douglas Veitch committed
14
import string
15
from math import floor,ceil,log,pow
16
import sys
17
import random
18
from itertools import permutations
19
import shutil
20
import numpy as np
21 22 23 24 25

# We use the GLUE pipeline utilities to construct classes for each
# type of job. Each class has inputs and outputs, which are used to
# join together types of jobs into a DAG.

John Douglas Veitch's avatar
John Douglas Veitch committed
26 27 28 29
class Event():
  """
  Represents a unique event to run on
  """
John Douglas Veitch's avatar
John Douglas Veitch committed
30
  new_id=itertools.count().next
31
  def __init__(self,trig_time=None,SimInspiral=None,SimBurst=None,SnglInspiral=None,CoincInspiral=None,event_id=None,timeslide_dict=None,GID=None,ifos=None, duration=None,srate=None,trigSNR=None,fhigh=None,horizon_distance=None):
John Douglas Veitch's avatar
John Douglas Veitch committed
32
    self.trig_time=trig_time
John Douglas Veitch's avatar
John Douglas Veitch committed
33
    self.injection=SimInspiral
34
    self.burstinjection=SimBurst
John Douglas Veitch's avatar
John Douglas Veitch committed
35
    self.sngltrigger=SnglInspiral
36 37 38 39
    if timeslide_dict is None:
      self.timeslides={}
    else:
      self.timeslides=timeslide_dict
40 41
    self.GID=GID
    self.coinctrigger=CoincInspiral
42 43 44 45
    if ifos is None:
      self.ifos = []
    else:
      self.ifos = ifos
46 47
    self.duration = duration
    self.srate = srate
48
    self.trigSNR = trigSNR
49
    self.fhigh = fhigh
50
    self.horizon_distance = horizon_distance
John Douglas Veitch's avatar
John Douglas Veitch committed
51 52 53
    if event_id is not None:
        self.event_id=event_id
    else:
John Douglas Veitch's avatar
John Douglas Veitch committed
54 55 56
        self.event_id=Event.new_id()
    if self.injection is not None:
        self.trig_time=self.injection.get_end()
57
        if event_id is None: self.event_id=int(str(self.injection.simulation_id).split(':')[2])
58 59 60
    if self.burstinjection is not None:
        self.trig_time=self.burstinjection.get_end()
        if event_id is None: self.event_id=int(str(self.burstinjection.simulation_id).split(':')[2])
John Douglas Veitch's avatar
John Douglas Veitch committed
61
    if self.sngltrigger is not None:
62
        self.trig_time=self.sngltrigger.get_end()
John Douglas Veitch's avatar
John Douglas Veitch committed
63
        self.event_id=int(str(self.sngltrigger.event_id).split(':')[2])
64 65 66 67
    if self.coinctrigger is not None:
        self.trig_time=self.coinctrigger.end_time + 1.0e-9 * self.coinctrigger.end_time_ns
    if self.GID is not None:
        self.event_id=int(''.join(i for i in self.GID if i.isdigit()))
68 69 70 71 72 73 74
    self.engine_opts={}
  def set_engine_option(self,opt,val):
    """
    Can set event-specific options for the engine nodes
    using this option, e.g. ev.set_engine_option('time-min','1083759273')
    """
    self.engine_opts[opt]=val
John Douglas Veitch's avatar
John Douglas Veitch committed
75 76

dummyCacheNames=['LALLIGO','LALVirgo','LALAdLIGO','LALAdVirgo']
John Douglas Veitch's avatar
John Douglas Veitch committed
77

78
def readLValert(threshold_snr=None,gid=None,flow=40.0,gracedb="gracedb",basepath="./",downloadpsd=True):
79
  """
80
  Parse LV alert file, containing coinc, sngl, coinc_event_map.
81 82
  and create a list of Events as input for pipeline
  Based on Chris Pankow's script
83
  """
84
  output=[]
85 86
  from glue.ligolw import utils
  from glue.ligolw import lsctables
87
  from glue.ligolw import ligolw
Rory Smith's avatar
Rory Smith committed
88
  class PSDContentHandler(ligolw.LIGOLWContentHandler):
89
    pass
Rory Smith's avatar
Rory Smith committed
90
  lsctables.use_in(PSDContentHandler)
91 92
  from glue.ligolw import param
  from glue.ligolw import array
93
  import subprocess
Rory Smith's avatar
Rory Smith committed
94
  from lal import series as lalseries
95
  from subprocess import Popen, PIPE
96 97
  cwd=os.getcwd()
  os.chdir(basepath)
98
  print "%s download %s coinc.xml"%(gracedb,gid)
Vivien Raymond's avatar
Vivien Raymond committed
99
  subprocess.call([gracedb,"download", gid ,"coinc.xml"])
Rory Smith's avatar
Rory Smith committed
100
  xmldoc=utils.load_filename("coinc.xml",contenthandler = PSDContentHandler)
101
  coinctable = lsctables.CoincInspiralTable.get_table(xmldoc)
102
  coinc_events = [event for event in coinctable]
103
  sngltable = lsctables.SnglInspiralTable.get_table(xmldoc)
104
  sngl_events = [event for event in sngltable]
105 106 107
  #Issues to identify IFO with good data that did not produce a trigger
  #search_summary = lsctables.getTablesByType(xmldoc, lsctables.SearchSummaryTable)[0]
  #ifos = search_summary[0].ifos.split(",")
108 109
  #coinc_table = lsctables.getTablesByType(xmldoc, lsctables.CoincTable)[0]
  #ifos = coinc_table[0].instruments.split(",")
110
  trigSNR = 2.0*coinctable[0].snr #The factor of 2.0 is because detection pipelines recover SNR lower than PE can recover.
111
  # Parse PSD
112
  srate_psdfile=16384
113 114 115 116
  ifos=None
  if downloadpsd:
    print "gracedb download %s psd.xml.gz" % gid
    subprocess.call([gracedb,"download", gid ,"psd.xml.gz"])
Rory Smith's avatar
Rory Smith committed
117
    xmlpsd = lalseries.read_psd_xmldoc(utils.load_filename('psd.xml.gz',contenthandler = lalseries.PSDContentHandler))
118 119
    # Note: This finds the active IFOs by looking for available PSDs
    # Is there another way of getting this info?
120
    ifos = xmlpsd.keys()
121
  psdasciidic=None
122
  fhigh=None
123
  if os.path.exists("psd.xml.gz"):
124 125 126
    psdasciidic=get_xml_psds(os.path.realpath("./psd.xml.gz"),ifos,os.path.realpath('./PSDs'),end_time=None)
    combine=np.loadtxt(psdasciidic[psdasciidic.keys()[0]])
    srate_psdfile = pow(2.0, ceil( log(float(combine[-1][0]), 2) ) ) * 2
127
  else:
128
    print "Failed to gracedb download %s psd.xml.gz. lalinference will estimate the psd itself." % gid
129
  # Logic for template duration and sample rate disabled
130
  coinc_map = lsctables.CoincMapTable.get_table(xmldoc)
131 132
  for coinc in coinc_events:
    these_sngls = [e for e in sngl_events if e.event_id in [c.event_id for c in coinc_map if c.coinc_event_id == coinc.coinc_event_id] ]
133 134
    dur=[]
    srate=[]
135
    horizon_distance=[]
136
    for e in these_sngls:
137
      # Review: Replace this with a call to LALSimulation function at some point
138 139 140
      p=Popen(["lalapps_chirplen","--flow",str(flow),"-m1",str(e.mass1),"-m2",str(e.mass2)],stdout=PIPE, stderr=PIPE, stdin=PIPE)
      strlen = p.stdout.read()
      dur.append(pow(2.0, ceil( log(max(8.0,float(strlen.splitlines()[2].split()[5]) + 2.0), 2) ) ) )
141
      srate.append(pow(2.0, ceil( log(float(strlen.splitlines()[1].split()[5]), 2) ) ) * 2 )
142 143 144 145 146 147 148
      snr = e.snr
      eff_dist = e.eff_distance
      if threshold_snr is not None:
          if snr > threshold_snr:
              horizon_distance.append(eff_dist * snr/threshold_snr)
          else:
              horizon_distance.append(2 * eff_dist)
149 150 151 152
    if max(srate)<srate_psdfile:
      srate = max(srate)
    else:
      srate = srate_psdfile
Vivien Raymond's avatar
Vivien Raymond committed
153
      fhigh = srate_psdfile/2.0 * 0.95 # Because of the drop-off near Nyquist of the PSD from gstlal
154 155 156 157
    horizon_distance = max(horizon_distance) if len(horizon_distance) > 0 else None
    ev=Event(CoincInspiral=coinc, GID=gid, ifos = ifos, duration = max(dur), srate = srate,
             trigSNR = trigSNR, fhigh = fhigh, horizon_distance=horizon_distance)
    output.append(ev)
158

159
  print "Found %d coinc events in table." % len(coinc_events)
160
  os.chdir(cwd)
161 162
  return output

163 164 165 166 167 168 169
def open_pipedown_database(database_filename,tmp_space):
    """
    Open the connection to the pipedown database
    """
    if not os.access(database_filename,os.R_OK):
	raise Exception('Unable to open input file: %s'%(database_filename))
    from glue.ligolw import dbtables
170
    import sqlite3
171 172 173 174
    working_filename=dbtables.get_connection_filename(database_filename,tmp_path=tmp_space)
    connection = sqlite3.connect(working_filename)
    if tmp_space:
	dbtables.set_temp_store_directory(connection,tmp_space)
175
    #dbtables.DBTable_set_connection(connection)
176
    return (connection,working_filename)
177

178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220
def get_zerolag_lloid(database_connection, dumpfile=None, gpsstart=None, gpsend=None, max_cfar=-1, min_cfar=-1):
	"""
	Returns a list of Event objects
	from pipedown data base. Can dump some stats to dumpfile if given,
	and filter by gpsstart and gpsend to reduce the nunmber or specify
	max_cfar to select by combined FAR
	"""
	output={}
	if gpsstart is not None: gpsstart=float(gpsstart)
	if gpsend is not None: gpsend=float(gpsend)
	# Get coincs
	get_coincs = "SELECT sngl_inspiral.end_time+sngl_inspiral.end_time_ns*1e-9,sngl_inspiral.ifo,coinc_event.coinc_event_id,sngl_inspiral.snr,sngl_inspiral.chisq,coinc_inspiral.combined_far \
		FROM sngl_inspiral join coinc_event_map on (coinc_event_map.table_name=='sngl_inspiral' and coinc_event_map.event_id ==\
		sngl_inspiral.event_id) join coinc_event on (coinc_event.coinc_event_id==coinc_event_map.coinc_event_id) \
		join coinc_inspiral on (coinc_event.coinc_event_id==coinc_inspiral.coinc_event_id) \
        WHERE coinc_event.time_slide_id=='time_slide:time_slide_id:1'\
		"
	if gpsstart is not None:
		get_coincs=get_coincs+' and coinc_inspiral.end_time+coinc_inspiral.end_time_ns*1.0e-9 > %f'%(gpsstart)
	if gpsend is not None:
		get_coincs=get_coincs+' and coinc_inspiral.end_time+coinc_inspiral.end_time_ns*1.0e-9 < %f'%(gpsend)
	if max_cfar !=-1:
		get_coincs=get_coincs+' and coinc_inspiral.combined_far < %f'%(max_cfar)
	if min_cfar != -1:
		get_coincs=get_coincs+' and coinc_inspiral.combined_far > %f'%(min_cfar)
	db_out=database_connection.cursor().execute(get_coincs)
    	extra={}
	for (sngl_time, ifo, coinc_id, snr, chisq, cfar) in db_out:
      		coinc_id=int(coinc_id.split(":")[-1])
	  	if not coinc_id in output.keys():
			output[coinc_id]=Event(trig_time=sngl_time,timeslide_dict={},event_id=int(coinc_id))
			extra[coinc_id]={}
		output[coinc_id].timeslides[ifo]=0
		output[coinc_id].ifos.append(ifo)
		extra[coinc_id][ifo]={'snr':snr,'chisq':chisq,'cfar':cfar}
	if dumpfile is not None:
		fh=open(dumpfile,'w')
		for co in output.keys():
			for ifo in output[co].ifos:
				fh.write('%s %s %s %s %s %s %s\n'%(str(co),ifo,str(output[co].trig_time),str(output[co].timeslides[ifo]),str(extra[co][ifo]['snr']),str(extra[co][ifo]['chisq']),str(extra[co][ifo]['cfar'])))
		fh.close()
	return output.values()

221
def get_zerolag_pipedown(database_connection, dumpfile=None, gpsstart=None, gpsend=None, max_cfar=-1, min_cfar=-1):
222 223 224 225 226 227 228 229 230 231 232 233 234 235
	"""
	Returns a list of Event objects
	from pipedown data base. Can dump some stats to dumpfile if given,
	and filter by gpsstart and gpsend to reduce the nunmber or specify
	max_cfar to select by combined FAR
	"""
	output={}
	if gpsstart is not None: gpsstart=float(gpsstart)
	if gpsend is not None: gpsend=float(gpsend)
	# Get coincs
	get_coincs = "SELECT sngl_inspiral.end_time+sngl_inspiral.end_time_ns*1e-9,sngl_inspiral.ifo,coinc_event.coinc_event_id,sngl_inspiral.snr,sngl_inspiral.chisq,coinc_inspiral.combined_far \
		FROM sngl_inspiral join coinc_event_map on (coinc_event_map.table_name=='sngl_inspiral' and coinc_event_map.event_id ==\
		sngl_inspiral.event_id) join coinc_event on (coinc_event.coinc_event_id==coinc_event_map.coinc_event_id) \
		join coinc_inspiral on (coinc_event.coinc_event_id==coinc_inspiral.coinc_event_id) \
236
		WHERE coinc_event.time_slide_id=='time_slide:time_slide_id:10049'\
237 238
		"
	if gpsstart is not None:
239
		get_coincs=get_coincs+' and coinc_inspiral.end_time+coinc_inspiral.end_time_ns*1.0e-9 > %f'%(gpsstart)
240
	if gpsend is not None:
241
		get_coincs=get_coincs+' and coinc_inspiral.end_time+coinc_inspiral.end_time_ns*1.0e-9 < %f'%(gpsend)
242 243
	if max_cfar !=-1:
		get_coincs=get_coincs+' and coinc_inspiral.combined_far < %f'%(max_cfar)
244 245
	if min_cfar != -1:
		get_coincs=get_coincs+' and coinc_inspiral.combined_far > %f'%(min_cfar)
246
	db_out=database_connection.cursor().execute(get_coincs)
John Douglas Veitch's avatar
John Douglas Veitch committed
247
    	extra={}
248
	for (sngl_time, ifo, coinc_id, snr, chisq, cfar) in db_out:
John Douglas Veitch's avatar
John Douglas Veitch committed
249 250
      		coinc_id=int(coinc_id.split(":")[-1])
	  	if not coinc_id in output.keys():
251
			output[coinc_id]=Event(trig_time=sngl_time,timeslide_dict={},event_id=int(coinc_id))
John Douglas Veitch's avatar
John Douglas Veitch committed
252 253 254 255
			extra[coinc_id]={}
		output[coinc_id].timeslides[ifo]=0
		output[coinc_id].ifos.append(ifo)
		extra[coinc_id][ifo]={'snr':snr,'chisq':chisq,'cfar':cfar}
256 257 258 259 260 261
	if dumpfile is not None:
		fh=open(dumpfile,'w')
		for co in output.keys():
			for ifo in output[co].ifos:
				fh.write('%s %s %s %s %s %s %s\n'%(str(co),ifo,str(output[co].trig_time),str(output[co].timeslides[ifo]),str(extra[co][ifo]['snr']),str(extra[co][ifo]['chisq']),str(extra[co][ifo]['cfar'])))
		fh.close()
262
	return output.values()
263

264
def get_timeslides_pipedown(database_connection, dumpfile=None, gpsstart=None, gpsend=None, max_cfar=-1):
265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280
	"""
	Returns a list of Event objects
	with times and timeslide offsets
	"""
	output={}
	if gpsstart is not None: gpsstart=float(gpsstart)
	if gpsend is not None: gpsend=float(gpsend)
	db_segments=[]
	sql_seg_query="SELECT search_summary.out_start_time, search_summary.out_end_time from search_summary join process on process.process_id==search_summary.process_id where process.program=='thinca'"
	db_out = database_connection.cursor().execute(sql_seg_query)
	for d in db_out:
		if d not in db_segments:
			db_segments.append(d)
	seglist=segments.segmentlist([segments.segment(d[0],d[1]) for d in db_segments])
	db_out_saved=[]
	# Get coincidences
281
	get_coincs="SELECT sngl_inspiral.end_time+sngl_inspiral.end_time_ns*1e-9,time_slide.offset,sngl_inspiral.ifo,coinc_event.coinc_event_id,sngl_inspiral.snr,sngl_inspiral.chisq,coinc_inspiral.combined_far \
282
		    FROM sngl_inspiral join coinc_event_map on (coinc_event_map.table_name == 'sngl_inspiral' and coinc_event_map.event_id \
283 284
		    == sngl_inspiral.event_id) join coinc_event on (coinc_event.coinc_event_id==coinc_event_map.coinc_event_id) join time_slide\
		    on (time_slide.time_slide_id == coinc_event.time_slide_id and time_slide.instrument==sngl_inspiral.ifo)\
285
		    join coinc_inspiral on (coinc_inspiral.coinc_event_id==coinc_event.coinc_event_id) where coinc_event.time_slide_id!='time_slide:time_slide_id:10049'"
John Douglas Veitch's avatar
John Douglas Veitch committed
286
	joinstr = ' and '
287
	if gpsstart is not None:
288
		get_coincs=get_coincs+ joinstr + ' coinc_inspiral.end_time+coinc_inspiral.end_time_ns*1e-9 > %f'%(gpsstart)
289
	if gpsend is not None:
290
		get_coincs=get_coincs+ joinstr+' coinc_inspiral.end_time+coinc_inspiral.end_time_ns*1e-9 <%f'%(gpsend)
291 292
	if max_cfar!=-1:
		get_coincs=get_coincs+joinstr+' coinc_inspiral.combined_far < %f'%(max_cfar)
293
	db_out=database_connection.cursor().execute(get_coincs)
294 295
	from pylal import SnglInspiralUtils
	extra={}
296
	for (sngl_time, slide, ifo, coinc_id, snr, chisq, cfar) in db_out:
297 298 299 300 301 302 303 304 305
		coinc_id=int(coinc_id.split(":")[-1])
		seg=filter(lambda seg:sngl_time in seg,seglist)[0]
		slid_time = SnglInspiralUtils.slideTimeOnRing(sngl_time,slide,seg)
		if not coinc_id in output.keys():
			output[coinc_id]=Event(trig_time=slid_time,timeslide_dict={},event_id=int(coinc_id))
			extra[coinc_id]={}
		output[coinc_id].timeslides[ifo]=slid_time-sngl_time
		output[coinc_id].ifos.append(ifo)
		extra[coinc_id][ifo]={'snr':snr,'chisq':chisq,'cfar':cfar}
306 307 308 309 310 311
	if dumpfile is not None:
		fh=open(dumpfile,'w')
		for co in output.keys():
			for ifo in output[co].ifos:
				fh.write('%s %s %s %s %s %s %s\n'%(str(co),ifo,str(output[co].trig_time),str(output[co].timeslides[ifo]),str(extra[co][ifo]['snr']),str(extra[co][ifo]['chisq']),str(extra[co][ifo]['cfar'])))
		fh.close()
312
	return output.values()
313

314 315 316 317 318 319 320 321
def mkdirs(path):
  """
  Helper function. Make the given directory, creating intermediate
  dirs if necessary, and don't complain about it already existing.
  """
  if os.access(path,os.W_OK) and os.path.isdir(path): return
  else: os.makedirs(path)

John Douglas Veitch's avatar
John Douglas Veitch committed
322 323 324
def chooseEngineNode(name):
  if name=='lalinferencenest':
    return LALInferenceNestNode
325 326
  if name=='lalinferenceburst':
    return LALInferenceBurstNode
John Douglas Veitch's avatar
John Douglas Veitch committed
327 328
  if name=='lalinferencemcmc':
    return LALInferenceMCMCNode
329
  if name=='lalinferencebambi' or name=='lalinferencebambimpi':
330
    return LALInferenceBAMBINode
331 332
  if name=='lalinferencedatadump':
    return LALInferenceDataDumpNode
333 334
  if name=='bayeswavepsd':
    return BayesWavePSDNode
John Douglas Veitch's avatar
John Douglas Veitch committed
335 336
  return EngineNode

337 338 339
def get_engine_name(cp):
    name=cp.get('analysis','engine')
    if name=='random':
340
        engine_list=['lalinferencenest','lalinferencemcmc','lalinferencebambimpi']
341 342 343 344 345 346 347 348 349
        if cp.has_option('input','gid'):
            gid=cp.get('input','gid')
            engine_number=int(''.join(i for i in gid if i.isdigit())) % 2
        else:
            engine_number=random.randint(0,1)
        return engine_list[engine_number]
    else:
        return name

350
def scan_timefile(timefile):
351 352 353 354 355 356 357 358 359 360 361 362
    import re
    p=re.compile('[\d.]+')
    times=[]
    timefilehandle=open(timefile,'r')
    for time in timefilehandle:
      if not p.match(time):
	continue
      if float(time) in times:
	print 'Skipping duplicate time %s'%(time)
	continue
      print 'Read time %s'%(time)
      times.append(float(time))
363 364
    timefilehandle.close()
    return times
365

366 367 368 369 370 371 372 373 374 375 376 377 378 379 380
def get_xml_psds(psdxml,ifos,outpath,end_time=None):
  """
  Get a psd.xml.gz file and:
  1) Reads it
  2) Converts PSD (10e-44) -> ASD ( ~10e-22)
  3) Checks the psd file contains all the IFO we want to analyze
  4) Writes down the ASDs into an ascii file for each IFO in psd.xml.gz. The name of the file contains the trigtime (if given) and the ifo name.
  Input:
    psdxml: psd.xml.gz file
    ifos: list of ifos used for the analysis
    outpath: path where the ascii ASD will be written to
    (end_time): trigtime for this event. Will be used a part of the ASD file name
  """
  lal=1
  from glue.ligolw import utils
381
  try:
Rory Smith's avatar
Rory Smith committed
382 383
    #from pylal import series
    from lal import series as series
384
    lal=0
385 386 387
  except ImportError:
    print "ERROR, cannot import pylal.series in bppu/get_xml_psds()\n"
    exit(1)
388

389 390 391 392 393 394 395 396 397 398 399
  out={}
  if not os.path.isdir(outpath):
    os.makedirs(outpath)
  if end_time is not None:
    time=repr(float(end_time))
  else:
    time=''
  #check we don't already have ALL the psd files #
  got_all=1
  for ifo in ifos:
    path_to_ascii_psd=os.path.join(outpath,ifo+'_psd_'+time+'.txt')
400
    # Check we don't already have that ascii (e.g. because we are running parallel runs of the save event
401 402 403 404 405 406 407 408 409
    if os.path.isfile(path_to_ascii_psd):
      got_all*=1
    else:
      got_all*=0
  if got_all==1:
    #print "Already have PSD files. Nothing to do...\n"
    for ifo in ifos:
      out[ifo]=os.path.join(outpath,ifo+'_psd_'+time+'.txt')
    return out
410

411 412 413 414
  # We need to convert the PSD for one or more IFOS. Open the file
  if not os.path.isfile(psdxml):
    print "ERROR: impossible to open the psd file %s. Exiting...\n"%psdxml
    sys.exit(1)
Rory Smith's avatar
Rory Smith committed
415
  xmlpsd =  series.read_psd_xmldoc(utils.load_filename(psdxml,contenthandler = series.PSDContentHandler))
416 417 418 419 420 421 422 423 424
  # Check the psd file contains all the IFOs we want to analize
  for ifo in ifos:
    if not ifo in [i.encode('ascii') for i in xmlpsd.keys()]:
      print "ERROR. The PSD for the ifo %s does not seem to be contained in %s\n"%(ifo,psdxml)
      sys.exit(1)
  #loop over ifos in psd xml file
  for instrument in xmlpsd.keys():
    #name of the ascii file we are going to write the PSD into
    path_to_ascii_psd=os.path.join(outpath,instrument.encode('ascii')+'_psd_'+time+'.txt')
425
    # Check we don't already have that ascii (e.g. because we are running parallel runs of the save event
426
    if os.path.isfile(path_to_ascii_psd):
427
      continue
428 429 430 431 432 433 434 435 436 437 438 439 440 441 442
    # get data for the IFO
    ifodata=xmlpsd[instrument]
    #check data is not empty
    if ifodata is None:
      continue
    # we have data. Get psd array
    if lal==0:
      #pylal stores the series in ifodata.data
      data=ifodata
    else:
      # lal stores it in ifodata.data.data
      data=ifodata.data
    # Fill a two columns array of (freq, psd) and save it in the ascii file
    f0=ifodata.f0
    deltaF=ifodata.deltaF
443

444
    combine=[]
445

Rory Smith's avatar
Rory Smith committed
446 447
    for i in np.arange(len(data.data.data)) :
      combine.append([f0+i*deltaF,np.sqrt(data.data.data[i])])
448
    np.savetxt(path_to_ascii_psd,combine)
449
    ifo=instrument.encode('ascii')
450 451 452
    # set node.psds dictionary with the path to the ascii files
    out[ifo]=os.path.join(outpath,ifo+'_psd_'+time+'.txt')
  return out
453

454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477
def get_trigger_chirpmass(gid=None,gracedb="gracedb"):
  from glue.ligolw import lsctables
  from glue.ligolw import ligolw
  from glue.ligolw import utils
  class PSDContentHandler(ligolw.LIGOLWContentHandler):
    pass
  lsctables.use_in(PSDContentHandler)
  import subprocess

  cwd=os.getcwd()
  subprocess.call([gracedb,"download", gid ,"coinc.xml"])
  xmldoc=utils.load_filename("coinc.xml",contenthandler = PSDContentHandler)
  coinctable = lsctables.CoincInspiralTable.get_table(xmldoc)
  coinc_events = [event for event in coinctable]
  sngltable = lsctables.SnglInspiralTable.get_table(xmldoc)
  sngl_events = [event for event in sngltable]
  coinc_map = lsctables.CoincMapTable.get_table(xmldoc)
  mass1 = []
  mass2 = []
  for coinc in coinc_events:
    these_sngls = [e for e in sngl_events if e.event_id in [c.event_id for c in coinc_map if c.coinc_event_id == coinc.coinc_event_id] ]
    for e in these_sngls:
      mass1.append(e.mass1)
      mass2.append(e.mass2)
478
  # check that trigger masses are identical in each IFO
479 480 481
  assert len(set(mass1)) == 1
  assert len(set(mass2)) == 1

482
  mchirp = (mass1[0]*mass2[0])**(3./5.) / ( (mass1[0] + mass2[0])**(1./5.) )
483 484 485 486
  os.remove("coinc.xml")

  return mchirp

487
def get_roq_mchirp_priors(path, roq_paths, roq_params, key, gid=None,sim_inspiral=None):
488

489 490
  ## XML and GID cannot be given at the same time
  ## sim_inspiral must already point at the right row
491
  mc_priors = {}
Vivien Raymond's avatar
Vivien Raymond committed
492

493 494 495
  if gid is not None and sim_inspiral is not None:
    print "Error in get_roq_mchirp_priors, cannot use both gid and sim_inspiral\n"
    sys.exit(1)
496 497 498 499 500 501

  for roq in roq_paths:
    params=os.path.join(path,roq,'params.dat')
    roq_params[roq]=np.genfromtxt(params,names=True)
    mc_priors[roq]=[float(roq_params[roq]['chirpmassmin']),float(roq_params[roq]['chirpmassmax'])]
  ordered_roq_paths=[item[0] for item in sorted(roq_params.items(), key=key)][::-1]
502 503
  # below is to construct non-overlapping mc priors for multiple roq mass-bin runs
  '''i=0
504 505 506 507 508 509 510
  for roq in ordered_roq_paths:
    if i>0:
      # change min, just set to the max of the previous one since we have already aligned it in the previous iteration of this loop
      #mc_priors[roq][0]+= (mc_priors[roq_lengths[i-1]][1]-mc_priors[roq][0])/2.
      mc_priors[roq][0]=mc_priors[ordered_roq_paths[i-1]][1]
    if i<len(roq_paths)-1:
      mc_priors[roq][1]-= (mc_priors[roq][1]- mc_priors[ordered_roq_paths[i+1]][0])/2.
511
    i+=1'''
512 513
  if gid is not None:
  	trigger_mchirp = get_trigger_chirpmass(gid)
514 515
  elif sim_inspiral is not None:
        trigger_mchirp = sim_inspiral.mchirp
516 517
  else:
	trigger_mchirp = None
518 519 520

  return mc_priors, trigger_mchirp

Vivien Raymond's avatar
Vivien Raymond committed
521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546
def get_roq_component_mass_priors(path, roq_paths, roq_params, key, gid=None,sim_inspiral=None):

  ## XML and GID cannot be given at the same time
  ## sim_inspiral must already point at the right row
  m1_priors = {}
  m2_priors = {}

  if gid is not None and sim_inspiral is not None:
    print "Error in get_roq_mchirp_priors, cannot use both gid and sim_inspiral\n"
    sys.exit(1)

  for roq in roq_paths:
    params=os.path.join(path,roq,'params.dat')
    roq_params[roq]=np.genfromtxt(params,names=True)
    m1_priors[roq]=[float(roq_params[roq]['mass1min']),float(roq_params[roq]['mass1max'])]
    m2_priors[roq]=[float(roq_params[roq]['mass2min']),float(roq_params[roq]['mass2max'])]

  if gid is not None:
    trigger_mchirp = get_trigger_chirpmass(gid)
  elif sim_inspiral is not None:
    trigger_mchirp = sim_inspiral.mchirp
  else:
    trigger_mchirp = None

  return m1_priors, m2_priors, trigger_mchirp

547
def get_roq_mass_freq_scale_factor(mc_priors, trigger_mchirp, force_flow=None):
548 549
  mc_max = mc_priors['4s'][1]
  mc_min = mc_priors['128s'][0]
550 551 552 553 554 555 556 557
  scale_factor = 1.
  if force_flow == None:
     if trigger_mchirp >= mc_max:
        scale_factor = 2.**(floor(trigger_mchirp/mc_max))
     if trigger_mchirp <= mc_min:
        scale_factor = (2./3.)**(ceil(trigger_mchirp/mc_min))
  else:
     scale_factor = 20./force_flow
558
  return scale_factor
559

560 561
def create_pfn_tuple(filename,protocol='file://',site='local'):
    return( (os.path.basename(filename),protocol+os.path.abspath(filename),site) )
562

Vivien Raymond's avatar
Vivien Raymond committed
563 564 565 566 567 568 569 570 571 572 573 574 575 576 577 578 579 580 581 582 583
def mchirp_from_components(m1, m2):
  return (m1*m2)**(3.0/5.0) / (m1+m2)**(1.0/5.0)

def Query_ROQ_Bounds_Type(path, roq_paths):
  # Assume that parametrization of ROQ bounds is independent of seglen; just look at first one
  import numpy as np
  roq = roq_paths[0]
  params = os.path.join(path,roq,'params.dat')
  roq_params0 = np.genfromtxt(params,names=True)
  roq_names_set = set(roq_params0.dtype.names)
  component_mass_bounds_set = set(['mass1min', 'mass1max', 'mass2min', 'mass2max'])
  chirp_mass_q_bounds_set = set(['chirpmassmin', 'chirpmassmax', 'qmin', 'qmax'])
  if roq_names_set.issuperset(component_mass_bounds_set):
    roq_bounds = 'component_mass'
  elif roq_names_set.issuperset(chirp_mass_q_bounds_set):
    roq_bounds = 'chirp_mass_q'
  else:
    print 'Invalid bounds for ROQ. Ether (m1,m2) or (mc,q) bounds are supported.'
    sys.exit(1)
  return roq_bounds

584
class LALInferencePipelineDAG(pipeline.CondorDAG):
585
  def __init__(self,cp,dax=False,first_dag=True,previous_dag=None,site='local'):
586 587
    self.subfiles=[]
    self.config=cp
588
    self.engine=get_engine_name(cp)
John Douglas Veitch's avatar
John Douglas Veitch committed
589
    self.EngineNode=chooseEngineNode(self.engine)
590
    self.site=site
591
    if cp.has_option('paths','basedir'):
John Douglas Veitch's avatar
John Douglas Veitch committed
592
      self.basepath=cp.get('paths','basedir')
593 594 595
    else:
      self.basepath=os.getcwd()
      print 'No basepath specified, using current directory: %s'%(self.basepath)
596
    mkdirs(self.basepath)
597 598
    if dax:
        os.chdir(self.basepath)
599
    self.posteriorpath=os.path.join(self.basepath,'posterior_samples')
John Douglas Veitch's avatar
John Douglas Veitch committed
600
    mkdirs(self.posteriorpath)
601 602 603 604 605 606 607 608 609 610 611 612
    if first_dag:
      daglogdir=cp.get('paths','daglogdir')
      mkdirs(daglogdir)
      self.daglogfile=os.path.join(daglogdir,'lalinference_pipeline-'+str(uuid.uuid1())+'.log')
      pipeline.CondorDAG.__init__(self,self.daglogfile,dax=dax)
    elif not first_dag and previous_dag is not None:
      daglogdir=cp.get('paths','daglogdir')
      mkdirs(daglogdir)
      self.daglogfile=os.path.join(daglogdir,'lalinference_pipeline-'+str(uuid.uuid1())+'.log')
      pipeline.CondorDAG.__init__(self,self.daglogfile,dax=dax)
      for node in previous_dag.get_nodes():
        self.add_node(node)
613
    if cp.has_option('paths','cachedir'):
John Douglas Veitch's avatar
John Douglas Veitch committed
614
      self.cachepath=cp.get('paths','cachedir')
615 616
    else:
      self.cachepath=os.path.join(self.basepath,'caches')
617
    mkdirs(self.cachepath)
618
    if cp.has_option('paths','logdir'):
John Douglas Veitch's avatar
John Douglas Veitch committed
619
      self.logpath=cp.get('paths','logdir')
620 621
    else:
      self.logpath=os.path.join(self.basepath,'log')
622
    mkdirs(self.logpath)
623
    if cp.has_option('analysis','ifos'):
624
      self.ifos=ast.literal_eval(cp.get('analysis','ifos'))
625 626 627
    else:
      self.ifos=['H1','L1','V1']
    self.segments={}
628 629 630 631
    if cp.has_option('datafind','veto-categories'):
      self.veto_categories=cp.get('datafind','veto-categories')
    else: self.veto_categories=[]
    for ifo in self.ifos:
632
      self.segments[ifo]=[]
633 634 635
    self.computeroqweightsnode={}
    self.bayeslinenode={}
    self.bayeswavepsdnode={}
636
    self.dq={}
637
    self.frtypes=ast.literal_eval(cp.get('datafind','types'))
638
    self.channels=ast.literal_eval(cp.get('data','channels'))
John Douglas Veitch's avatar
John Douglas Veitch committed
639
    self.use_available_data=False
640
    self.webdir=cp.get('paths','webdir')
641 642 643 644
    if cp.has_option('analysis','dataseed'):
      self.dataseed=cp.getint('analysis','dataseed')
    else:
      self.dataseed=None
645
    # Set up necessary job files.
646
    self.prenodes={}
647
    self.datafind_job = pipeline.LSCDataFindJob(self.cachepath,self.logpath,self.config,dax=self.is_dax())
648
    self.datafind_job.add_opt('url-type','file')
649 650
    if cp.has_option('analysis','accounting_group'):
      self.datafind_job.add_condor_cmd('accounting_group',cp.get('analysis','accounting_group'))
651 652
    if cp.has_option('analysis','accounting_group_user'):
      self.datafind_job.add_condor_cmd('accounting_group_user',cp.get('analysis','accounting_group_user'))
653
    self.datafind_job.set_sub_file(os.path.abspath(os.path.join(self.basepath,'datafind.sub')))
654
    self.preengine_job = EngineJob(self.config, os.path.join(self.basepath,'prelalinference.sub'),self.logpath,engine='lalinferencedatadump',ispreengine=True,dax=self.is_dax())
655 656
    self.preengine_job.set_grid_site('local')
    self.preengine_job.set_universe('vanilla')
657 658 659 660 661 662
    if self.config.has_option('condor','computeroqweights'):
      self.computeroqweights_job = ROMJob(self.config,os.path.join(self.basepath,'computeroqweights.sub'),self.logpath,dax=self.is_dax())
      self.computeroqweights_job.set_grid_site('local')
    if self.config.has_option('condor','bayesline'):
      self.bayesline_job = BayesLineJob(self.config,os.path.join(self.basepath,'bayesline.sub'),self.logpath,dax=self.is_dax())
      self.bayesline_job.set_grid_site('local')
663 664 665 666 667
    self.bayeswavepsd_job={}
    if self.config.has_option('condor','bayeswave'):
      for ifo in self.ifos:
         self.bayeswavepsd_job[ifo] = BayesWavePSDJob(self.config,os.path.join(self.basepath,'bayeswavepsd_%s.sub'%(ifo)),self.logpath,dax=self.is_dax())
         self.bayeswavepsd_job[ifo].set_grid_site('local')
668 669 670 671
    # Need to create a job file for each IFO combination
    self.engine_jobs={}
    ifocombos=[]
    for N in range(1,len(self.ifos)+1):
672
        for a in permutations(self.ifos,N):
673 674
            ifocombos.append(a)
    for ifos in ifocombos:
675
        self.engine_jobs[ifos] = EngineJob(self.config, os.path.join(self.basepath,'engine_%s.sub'%(reduce(lambda x,y:x+y, map(str,ifos)))),self.logpath,engine=self.engine,dax=self.is_dax(), site=site)
676
    self.results_page_job = ResultsPageJob(self.config,os.path.join(self.basepath,'resultspage.sub'),self.logpath,dax=self.is_dax())
677
    self.results_page_job.set_grid_site('local')
678
    self.cotest_results_page_job = ResultsPageJob(self.config,os.path.join(self.basepath,'resultspagecoherent.sub'),self.logpath,dax=self.is_dax())
679
    self.cotest_results_page_job.set_grid_site('local')
680
    self.merge_job = MergeNSJob(self.config,os.path.join(self.basepath,'merge_runs.sub'),self.logpath,dax=self.is_dax())
681
    self.merge_job.set_grid_site('local')
682
    self.coherence_test_job = CoherenceTestJob(self.config,os.path.join(self.basepath,'coherence_test.sub'),self.logpath,dax=self.is_dax())
683
    self.coherence_test_job.set_grid_site('local')
684
    self.gracedbjob = GraceDBJob(self.config,os.path.join(self.basepath,'gracedb.sub'),self.logpath,dax=self.is_dax())
685
    self.gracedbjob.set_grid_site('local')
686
    # Process the input to build list of analyses to do
John Douglas Veitch's avatar
Working  
John Douglas Veitch committed
687
    self.events=self.setup_from_inputs()
688

689
    # Sanity checking
John Douglas Veitch's avatar
Working  
John Douglas Veitch committed
690
    if len(self.events)==0:
691 692
      print 'No input events found, please check your config if you expect some events'
    self.times=[e.trig_time for e in self.events]
693

694
    # Set up the segments
695
    if not (self.config.has_option('input','gps-start-time') and self.config.has_option('input','gps-end-time')) and len(self.times)>0:
696
      (mintime,maxtime)=self.get_required_data(self.times)
697 698 699 700
      if not self.config.has_option('input','gps-start-time'):
        self.config.set('input','gps-start-time',str(int(floor(mintime))))
      if not self.config.has_option('input','gps-end-time'):
        self.config.set('input','gps-end-time',str(int(ceil(maxtime))))
701
    self.add_science_segments()
702

703
    # Save the final configuration that is being used
704
    # first to the run dir
705 706
    conffilename=os.path.join(self.basepath,'config.ini')
    with open(conffilename,'wb') as conffile:
John Douglas Veitch's avatar
John Douglas Veitch committed
707
      self.config.write(conffile)
708 709 710 711
    if self.config.has_option('paths','webdir'):
      mkdirs(self.config.get('paths','webdir'))
      with open(os.path.join(self.config.get('paths','webdir'),'config.ini'),'wb') as conffile:
        self.config.write(conffile)
712

713
    # Generate the DAG according to the config given
714
    for event in self.events: self.add_full_analysis(event)
715
    self.add_skyarea_followup()
716 717 718
    if self.config.has_option('analysis','upload-to-gracedb'):
      if self.config.getboolean('analysis','upload-to-gracedb'):
        self.add_gracedb_FITSskymap_upload(self.events[0],engine=self.engine)
719 720 721 722 723 724 725 726 727
    self.dagfilename="lalinference_%s-%s"%(self.config.get('input','gps-start-time'),self.config.get('input','gps-end-time'))
    self.set_dag_file(self.dagfilename)
    if self.is_dax():
      self.set_dax_file(self.dagfilename)

  def add_skyarea_followup(self):
    # Add skyarea jobs if the executable is given
    # Do one for each results page for now
    if self.config.has_option('condor','skyarea'):
728 729
      self.skyareajob=SkyAreaJob(self.config,os.path.join(self.basepath,'skyarea.sub'),self.logpath,dax=self.is_dax())
      respagenodes=filter(lambda x: isinstance(x,ResultsPageNode) ,self.get_nodes())
730 731 732 733
      if self.engine=='lalinferenceburst':
          prefix='LIB_'
      else:
          prefix='LALInference_'
734
      for p in respagenodes:
735
          skyareanode=SkyAreaNode(self.skyareajob,prefix=prefix)
736
          skyareanode.add_resultspage_parent(p)
737
          skyareanode.set_ifos(p.ifos)
738
          self.add_node(skyareanode)
739

740
  def add_full_analysis(self,event):
741
    if self.engine=='lalinferencenest' or  self.engine=='lalinferenceburst':
742
      result=self.add_full_analysis_lalinferencenest(event)
743
    elif self.engine=='lalinferencemcmc':
744
      result=self.add_full_analysis_lalinferencemcmc(event)
745
    elif self.engine=='lalinferencebambi' or self.engine=='lalinferencebambimpi':
746 747 748
      result=self.add_full_analysis_lalinferencebambi(event)
    return result

749 750 751 752 753 754 755 756 757
  def create_frame_pfn_file(self):
    """
    Create a pegasus cache file name, uses inspiralutils
    """
    import inspiralutils as iu
    gpsstart=self.config.get('input','gps-start-time')
    gpsend=self.config.get('input','gps-end-time')
    pfnfile=iu.create_frame_pfn_file(self.frtypes,gpsstart,gpsend)
    return pfnfile
758

John Douglas Veitch's avatar
John Douglas Veitch committed
759 760
  def get_required_data(self,times):
    """
John Douglas Veitch's avatar
John Douglas Veitch committed
761
    Calculate the data that will be needed to process all events
John Douglas Veitch's avatar
John Douglas Veitch committed
762
    """
763
    #psdlength = self.config.getint('input','max-psd-length')
764
    padding=self.config.getint('input','padding')
765 766 767 768 769 770
    if self.config.has_option('engine','seglen') or self.config.has_option('lalinference','seglen'):
      if self.config.has_option('engine','seglen'):
        seglen = self.config.getint('engine','seglen')
      if self.config.has_option('lalinference','seglen'):
        seglen = self.config.getint('lalinference','seglen')

771
      if os.path.isfile(os.path.join(self.basepath,'psd.xml.gz')):
772 773 774
        psdlength = 0
      else:
        psdlength = 32*seglen
775 776
    else:
      seglen = max(e.duration for e in self.events)
777
      if os.path.isfile(os.path.join(self.basepath,'psd.xml.gz')):
778 779 780 781
        psdlength = 0
      else:
        psdlength = 32*seglen
    # Assume that the data interval is (end_time - seglen -padding , end_time + psdlength +padding )
782
    # -> change to (trig_time - seglen - padding - psdlength + 2 , trig_time + padding + 2) to estimate the psd before the trigger for online follow-up.
783
    # Also require padding before start time
784
    return (min(times)-padding-seglen-psdlength+2,max(times)+padding+2)
John Douglas Veitch's avatar
John Douglas Veitch committed
785

786 787 788 789 790
  def setup_from_times(self,times):
    """
    Generate a DAG from a list of times
    """
    for time in self.times:
791
      self.add_full_analysis(Event(trig_time=time))
792

793 794 795 796 797 798 799 800 801 802 803 804 805 806 807 808 809 810 811 812 813 814 815 816
  def select_events(self):
    """
    Read events from the config parser. Understands both ranges and comma separated events, or combinations
    eg. events=[0,1,5:10,21] adds to the analysis the events: 0,1,5,6,7,8,9,10 and 21
    """
    events=[]
    times=[]
    raw_events=self.config.get('input','events').replace('[','').replace(']','').split(',')
    for raw_event in raw_events:
        if ':' in raw_event:
            limits=raw_event.split(':')
            if len(limits) != 2:
                print "Error: in event config option; ':' must separate two numbers."
                exit(0)
            low=int(limits[0])
            high=int(limits[1])
            if low>high:
                events.extend(range(int(high),int(low)+1))
            elif high>low:
                events.extend(range(int(low),int(high)+1))
        else:
            events.append(int(raw_event))
    return events

John Douglas Veitch's avatar
Working  
John Douglas Veitch committed
817 818 819 820 821 822 823
  def setup_from_inputs(self):
    """
    Scan the list of inputs, i.e.
    gps-time-file, injection-file, sngl-inspiral-file, coinc-inspiral-file, pipedown-database
    in the [input] section of the ini file.
    And process the events found therein
    """
824
    events=[]
825 826
    gpsstart=None
    gpsend=None
827 828 829 830
    if self.config.has_option('input','gps-start-time'):
      gpsstart=self.config.getfloat('input','gps-start-time')
    if self.config.has_option('input','gps-end-time'):
      gpsend=self.config.getfloat('input','gps-end-time')
831
    inputnames=['gps-time-file','burst-injection-file','injection-file','sngl-inspiral-file','coinc-inspiral-file','pipedown-db','gid','gstlal-db']