def test_add_why(self):
inferences = [vp.Inference(probability=0.5, relation=None,
name='Toin Coss', concept='Probability')]
vp.add_why(self.v, importance=0.6,
expires=datetime.datetime(2013, 1, 1),
inferences=inferences)
self.assertTrue(vp.valid_as_v2_0(self.v))
self.assertEqual(self.v.Why.attrib['importance'], str(0.6))
self.assertEqual(self.v.Why.Inference[0].attrib['probability'],
str(0.5))
self.assertEqual(self.v.Why.Inference[0].Name, 'Toin Coss')
def test_add_why(self):
inferences = [vp.Inference(probability=0.5, relation=None,
name='Toin Coss', concept='Probability')]
vp.add_why(self.v, importance=0.6,
expires=datetime.datetime(2013, 1, 1),
inferences=inferences)
self.assertTrue(vp.valid_as_v2_0(self.v))
self.assertEqual(self.v.Why.attrib['importance'], str(0.6))
self.assertEqual(self.v.Why.Inference[0].attrib['probability'],
str(0.5))
self.assertEqual(self.v.Why.Inference[0].Name, 'Toin Coss')
def set_why(self):
'''
Add Why section to voevent object.
'''
# Why section (optional) allows for speculation on probable
# astrophysical cause
if self.event['detected']:
vp.add_why(self.v,
inferences=vp.Inference(relation='detected',
name=self.event['name']))
else:
vp.add_why(self.v,
inferences=vp.Inference(name=self.event['name']))
# Prettyprint some sections for desk-checking:
print("\n***Here is your WhereWhen:***\n")
print(vp.prettystr(v.WhereWhen))
print("\n***And your What:***\n")
print(vp.prettystr(v.What))
# You would normally describe or reference your telescope / instrument here:
vp.add_how(v, descriptions='Discovered via 4PiSky',
references=vp.Reference('http://4pisky.org'))
# The 'Why' section is optional, allows for speculation on probable
# astrophysical cause
vp.add_why(v, importance=0.5,
inferences=vp.Inference(probability=0.1,
relation='identified',
name='GRB121212A',
concept='process.variation.burst;em.radio')
)
# We can also cite earlier VOEvents:
vp.add_citations(v,
vp.EventIvorn(
ivorn='ivo://astronomy.physics.science.org/super_exciting_events#101',
cite_type=vp.definitions.cite_types.followup))
# Check everything is schema compliant:
vp.assert_valid_as_v2_0(v)
output_filename = 'new_voevent_example.xml'
with open(output_filename, 'wb') as f:
vp.dump(v, f)
# We should also describe how this transient was detected, and refer to the name
# that Gaia have assigned it. Note that we can provide multiple descriptions
# (and/or references) here:
# In[ ]:
vp.add_how(v,
descriptions=['Scraped from the Gaia website', 'This is Gaia14adi'],
references=vp.Reference("http://gsaweb.ast.cam.ac.uk/alerts/"))
# ##And finally, ``Why``##
# Finally, we can provide some information about why this even might be scientifically interesting. Gaia haven't provided a classification, but we can at least incorporate the textual description:
# In[ ]:
vp.add_why(v)
v.Why.Description = "Fading source on top of 2MASS Galaxy (offset from bulge)"
# ##Check and save##
# Finally - and importantly, as discussed in the [VOEvent notes](http://voevent.readthedocs.org/en/latest/parse.html) - let's make sure that this event is really valid according to our schema:
# In[ ]:
vp.valid_as_v2_0(v)
# Great! We can now save it to disk:
# In[ ]:
with open('gaia.xml', 'w') as f:
vp.dump(v, f)
print("\n***Here is your WhereWhen:***\n")
print(vp.prettystr(v.WhereWhen))
print("\n***And your What:***\n")
print(vp.prettystr(v.What))
# You would normally describe or reference your telescope / instrument here:
vp.add_how(v,
descriptions='Discovered via 4PiSky',
references=vp.Reference('http://4pisky.org'))
# The 'Why' section is optional, allows for speculation on probable
# astrophysical cause
vp.add_why(v,
importance=0.5,
inferences=vp.Inference(probability=0.1,
relation='identified',
name='GRB121212A',
concept='process.variation.burst;em.radio'))
# We can also cite earlier VOEvents:
vp.add_citations(
v,
vp.EventIvorn(
ivorn='ivo://astronomy.physics.science.org/super_exciting_events#101',
cite_type=vp.definitions.cite_types.followup))
# Check everything is schema compliant:
vp.assert_valid_as_v2_0(v)
output_filename = 'new_voevent_example.xml'
with open(output_filename, 'wb') as f:
# that Gaia have assigned it. Note that we can provide multiple descriptions
# (and/or references) here:
# In[ ]:
vp.add_how(v, descriptions=['Scraped from the Gaia website',
'This is Gaia14adi'],
references=vp.Reference("http://gsaweb.ast.cam.ac.uk/alerts/"))
# ##And finally, ``Why``##
# Finally, we can provide some information about why this even might be scientifically interesting. Gaia haven't provided a classification, but we can at least incorporate the textual description:
# In[ ]:
vp.add_why(v)
v.Why.Description = "Fading source on top of 2MASS Galaxy (offset from bulge)"
# ##Check and save##
# Finally - and importantly, as discussed in the [VOEvent notes](http://voevent.readthedocs.org/en/latest/parse.html) - let's make sure that this event is really valid according to our schema:
# In[ ]:
vp.valid_as_v2_0(v)
# Great! We can now save it to disk:
# In[ ]:
def create_voevent(jsonfile=None, deployment=False, **kwargs):
""" template syntax for voeventparse creation of voevent
"""
required = [
'internalname', 'mjds', 'dm', 'width', 'snr', 'ra', 'dec', 'radecerr'
]
preferred = ['fluence', 'p_flux', 'importance', 'dmerr']
# set values
dd = kwargs.copy()
if jsonfile is not None: # as made by caltechdata.set_metadata
for k, v in trigger.items():
if k in required + preferred:
dd[k] = v
assert all([
k in dd for k in required
]), f'Input keys {list(dd.keys())} not complete (requires {required})'
# TODO: set this correctly
dt = time.Time(dd['mjds'], format='mjd').to_datetime(timezone=pytz.utc)
# create voevent instance
role = vp.definitions.roles.observation if deployment else vp.definitions.roles.test
v = vp.Voevent(
stream='', # TODO: check
stream_id=1,
role=role)
vp.set_who(v,
date=datetime.datetime.utcnow(),
author_ivorn="voevent.dsa-110.caltech.org") # TODO: check
vp.set_author(v,
title="DSA-110 Testing Node",
contactName="Casey Law",
contactEmail="*****@*****.**")
params = []
dm = vp.Param(name="dm",
value=str(dd['dm']),
unit="pc/cm^3",
ucd="phys.dispMeasure;em.radio.750-1500MHz",
dataType='float',
ac=True)
dm.Description = 'Dispersion Measure'
params.append(dm)
width = vp.Param(name="width",
value=str(dd['width']),
unit="ms",
ucd="time.duration;src.var.pulse",
dataType='float',
ac=True)
width.Description = 'Temporal width of burst'
params.append(width)
snr = vp.Param(name="snr",
value=str(dd['snr']),
ucd="stat.snr",
dataType='float',
ac=True)
snr.Description = 'Signal to noise ratio'
params.append(snr)
if 'fluence' in dd:
fluence = vp.Param(
name='fluence',
value=str(dd['fluence']),
unit='Jansky ms',
ucd='em.radio.750-1500MHz', # TODO: check
dataType='float',
ac=False)
fluence.Description = 'Fluence'
params.append(fluence)
if 'p_flux' in dd:
p_flux = vp.Param(name='peak_flux',
value=str(dd['p_flux']),
unit='Janskys',
ucd='em.radio.750-1500MHz',
dataType='float',
ac=True)
p_flux.Description = 'Peak Flux'
params.append(p_flux)
if 'dmerr' in dd:
dmerr = vp.Param(name="dm_error",
value=str(dd['dmerr']),
unit="pc/cm^3",
ucd="phys.dispMeasure;em.radio.750-1500MHz",
dataType='float',
ac=True)
dmerr.Description = 'Dispersion Measure error'
params.append(dmerr)
v.What.append(vp.Group(params=params, name='event parameters'))
vp.add_where_when(v,
coords=vp.Position2D(
ra=str(dd['ra']),
dec=str(dd['dec']),
err=str(dd['radecerr']),
units='deg',
system=vp.definitions.sky_coord_system.utc_fk5_geo),
obs_time=dt,
observatory_location='OVRO')
print("\n***Here is your WhereWhen:***\n")
print(vp.prettystr(v.WhereWhen))
print("\n***And your What:***\n")
print(vp.prettystr(v.What))
vp.add_how(v,
descriptions='Discovered with DSA-110',
references=vp.Reference('http://deepsynoptic.org'))
if 'importance' in dd:
vp.add_why(v, importance=str(dd['importance']))
else:
vp.add_why(v)
v.Why.Name = str(dd['internalname'])
vp.assert_valid_as_v2_0(v)
return v
def NewVOEvent(dm, dm_err, width, snr, flux, ra, dec, semiMaj, semiMin, ymw16, name, importance, utc, gl, gb):
z = dm/1200.0 #May change
errDeg = semiMaj/60.0
# Parse UTC
utc_YY = int(utc[:4])
utc_MM = int(utc[5:7])
utc_DD = int(utc[8:10])
utc_hh = int(utc[11:13])
utc_mm = int(utc[14:16])
utc_ss = float(utc[17:])
t = Time('T'.join([utc[:10], utc[11:]]), scale='utc', format='isot')
mjd = t.mjd
now = Time.now()
mjd_now = now.mjd
ivorn = ''.join([name, str(utc_hh), str(utc_mm), '/', str(mjd_now)])
v = vp.Voevent(stream='nl.astron.apertif/alert', stream_id=ivorn, role=vp.definitions.roles.test)
# v = vp.Voevent(stream='nl.astron.apertif/alert', stream_id=ivorn, role=vp.definitions.roles.observation)
# Author origin information
vp.set_who(v, date=datetime.datetime.utcnow(), author_ivorn="nl.astron")
# Author contact information
vp.set_author(v, title="ASTRON ALERT FRB Detector", contactName="Leon Oostrum", contactEmail="*****@*****.**", shortName="ALERT")
# Parameter definitions
#Apertif-specific observing configuration %%TODO: update parameters as necessary for new obs config
beam_sMa = vp.Param(name="beam_semi-major_axis", unit="MM", ucd="instr.beam;pos.errorEllipse;phys.angSize.smajAxis", ac=True, value=semiMaj)
beam_sma = vp.Param(name="beam_semi-minor_axis", unit="MM", ucd="instr.beam;pos.errorEllipse;phys.angSize.sminAxis", ac=True, value=semiMin)
beam_rot = vp.Param(name="beam_rotation_angle", value=0.0, unit="Degrees", ucd="instr.beam;pos.errorEllipse;instr.offset", ac=True)
tsamp = vp.Param(name="sampling_time", value=0.0496, unit="ms", ucd="time.resolution", ac=True)
bw = vp.Param(name="bandwidth", value=300.0, unit="MHz", ucd="instr.bandwidth", ac=True)
nchan = vp.Param(name="nchan", value="1536", dataType="int", ucd="meta.number;em.freq;em.bin", unit="None")
cf = vp.Param(name="centre_frequency", value=1400.0, unit="MHz", ucd="em.freq;instr", ac=True)
npol = vp.Param(name="npol", value="2", dataType="int", unit="None")
bits = vp.Param(name="bits_per_sample", value="8", dataType="int", unit="None")
gain = vp.Param(name="gain", value=1.0, unit="K/Jy", ac=True)
tsys = vp.Param(name="tsys", value=75.0, unit="K", ucd="phot.antennaTemp", ac=True)
backend = vp.Param(name="backend", value="ARTS")
# beam = vp.Param(name="beam", value= )
v.What.append(vp.Group(params=[beam_sMa, beam_sma, beam_rot, tsamp, bw, nchan, cf, npol, bits, gain, tsys, backend], name="observatory parameters"))
#Event parameters
DM = vp.Param(name="dm", ucd="phys.dispMeasure", unit="pc/cm^3", ac=True, value=dm )
# DM_err = vp.Param(name="dm_err", ucd="stat.error;phys.dispMeasure", unit="pc/cm^3", ac=True, value=dm_err)
Width = vp.Param(name="width", ucd="time.duration;src.var.pulse", unit="ms", ac=True, value=width)
SNR = vp.Param(name="snr", ucd="stat.snr", unit="None", ac=True, value=snr)
Flux = vp.Param(name="flux", ucd="phot.flux", unit="Jy", ac=True, value=flux)
Flux.Description = "Calculated from radiometer equation. Not calibrated."
Gl = vp.Param(name="gl", ucd="pos.galactic.lon", unit="Degrees", ac=True, value=gl)
Gb = vp.Param(name="gb", ucd="pos.galactic.lat", unit="Degrees", ac=True, value=gb)
v.What.append(vp.Group(params=[DM, Width, SNR, Flux, Gl, Gb], name="event parameters"))
# v.What.append(vp.Group(params=[DM, DM_err, Width, SNR, Flux, Gl, Gb], name="event parameters"))
#Advanced parameters (note, change script if using a differeing MW model)
mw_dm = vp.Param(name="MW_dm_limit", unit="pc/cm^3", ac=True, value=ymw16)
mw_model = vp.Param(name="galactic_electron_model", value="YMW16")
redshift_inferred = vp.Param(name="redshift_inferred", ucd="src.redshift", unit="None", value=z)
redshift_inferred.Description = "Redshift estimated using z = DM/1200.0 (Ioka 2003)"
v.What.append(vp.Group(params=[mw_dm, mw_model, redshift_inferred], name="advanced parameters"))
#WhereWhen
vp.add_where_when(v, coords=vp.Position2D(ra=ra, dec=dec, err=errDeg, units='deg', system=vp.definitions.sky_coord_system.utc_fk5_geo),
obs_time=datetime.datetime(utc_YY,utc_MM,utc_DD,utc_hh,utc_mm,int(utc_ss), tzinfo=pytz.UTC), observatory_location="WSRT")
#Why
vp.add_why(v, importance=imp)
v.Why.Name = name
if vp.valid_as_v2_0(v):
with open('%s.xml' % utc, 'wb') as f:
voxml = vp.dumps(v)
xmlstr = minidom.parseString(voxml).toprettyxml(indent=" ")
f.write(xmlstr)
print(vp.prettystr(v.Who))
print(vp.prettystr(v.What))
print(vp.prettystr(v.WhereWhen))
print(vp.prettystr(v.Why))
else:
print "Unable to write file %s.xml" % name
def _NewVOEvent(self, dm, dm_err, width, snr, flux, ra, dec, semiMaj, semiMin,
ymw16, name, importance, utc, gl, gb, gain,
dt=TSAMP.to(u.ms).value, delta_nu_MHz=(BANDWIDTH / NCHAN).to(u.MHz).value,
nu_GHz=1.37, posang=0, test=None):
"""
Create a VOEvent
:param float dm: Dispersion measure (pc cm**-3)
:param float dm_err: Error on DM (pc cm**-3)
:param float width: Pulse width (ms)
:param float snr: Signal-to-noise ratio
:param float flux: flux density (mJy)
:param float ra: Right ascension (deg)
:param float dec: Declination (deg)
:param float semiMaj: Localisation region semi-major axis (arcmin)
:param float semiMin: Localisation region semi-minor axis (arcmin)
:param float ymw16: YMW16 DM (pc cm**-3)
:param str name: Source name
:param float importance: Trigger importance (0-1)
:param str utc: UTC arrival time in ISOT format
:param float gl: Galactic longitude (deg)
:param float gb: Galactic latitude (deg)
:param float gain: Telescope gain (K Jy**-1)
:param float dt: Telescope time resolution (ms)
:param float delta_nu_MHz: Telescope frequency channel width (MHz)
:param float nu_GHz: Telescope centre frequency (GHz)
:param float posang: Localisation region position angle (deg)
:param bool test: Whether to send a test event or observation event
"""
z = dm / 1000.0 # May change
errDeg = semiMaj / 60.0
# Parse UTC
utc_YY = int(utc[:4])
utc_MM = int(utc[5:7])
utc_DD = int(utc[8:10])
utc_hh = int(utc[11:13])
utc_mm = int(utc[14:16])
utc_ss = float(utc[17:])
t = Time(utc, scale='utc', format='isot')
# IERS server is down, avoid using it
t.delta_ut1_utc = 0
mjd = t.mjd
ivorn = ''.join([name, str(utc_hh), str(utc_mm), '/', str(mjd)])
# use default value for test flag if not set
if test is None:
test = self.test
# Set role to either test or real observation
if test:
self.logger.info("Event type is test")
v = vp.Voevent(stream='nl.astron.apertif/alert', stream_id=ivorn,
role=vp.definitions.roles.test)
else:
self.logger.info("Event type is observation")
v = vp.Voevent(stream='nl.astron.apertif/alert', stream_id=ivorn,
role=vp.definitions.roles.observation)
# Author origin information
vp.set_who(v, date=datetime.datetime.utcnow(), author_ivorn="nl.astron")
# Author contact information
vp.set_author(v, title="ARTS FRB alert system", contactName="Leon Oostrum",
contactEmail="*****@*****.**", shortName="ALERT")
# Parameter definitions
# Apertif-specific observing configuration
beam_sMa = vp.Param(name="beam_semi-major_axis", unit="MM",
ucd="instr.beam;pos.errorEllipse;phys.angSize.smajAxis", ac=True, value=semiMaj)
beam_sma = vp.Param(name="beam_semi-minor_axis", unit="MM",
ucd="instr.beam;pos.errorEllipse;phys.angSize.sminAxis", ac=True, value=semiMin)
beam_rot = vp.Param(name="beam_rotation_angle", value=str(posang), unit="Degrees",
ucd="instr.beam;pos.errorEllipse;instr.offset", ac=True)
tsamp = vp.Param(name="sampling_time", value=str(dt), unit="ms", ucd="time.resolution", ac=True)
bw = vp.Param(name="bandwidth", value=str(delta_nu_MHz), unit="MHz", ucd="instr.bandwidth", ac=True)
nchan = vp.Param(name="nchan", value=str(NCHAN), dataType="int",
ucd="meta.number;em.freq;em.bin", unit="None")
cf = vp.Param(name="centre_frequency", value=str(1000 * nu_GHz), unit="MHz", ucd="em.freq;instr", ac=True)
npol = vp.Param(name="npol", value="2", dataType="int", unit="None")
bits = vp.Param(name="bits_per_sample", value="8", dataType="int", unit="None")
gain = vp.Param(name="gain", value=str(gain), unit="K/Jy", ac=True)
tsys = vp.Param(name="tsys", value=str(TSYS.to(u.Kelvin).value), unit="K", ucd="phot.antennaTemp", ac=True)
backend = vp.Param(name="backend", value="ARTS")
# beam = vp.Param(name="beam", value= )
v.What.append(vp.Group(params=[beam_sMa, beam_sma, beam_rot, tsamp,
bw, nchan, cf, npol, bits, gain, tsys, backend],
name="observatory parameters"))
# Event parameters
DM = vp.Param(name="dm", ucd="phys.dispMeasure", unit="pc/cm^3", ac=True, value=str(dm))
DM_err = vp.Param(name="dm_err", ucd="stat.error;phys.dispMeasure", unit="pc/cm^3", ac=True, value=str(dm_err))
Width = vp.Param(name="width", ucd="time.duration;src.var.pulse", unit="ms", ac=True, value=str(width))
SNR = vp.Param(name="snr", ucd="stat.snr", unit="None", ac=True, value=str(snr))
Flux = vp.Param(name="flux", ucd="phot.flux", unit="Jy", ac=True, value=str(flux))
Flux.Description = "Calculated from radiometer equation. Not calibrated."
Gl = vp.Param(name="gl", ucd="pos.galactic.lon", unit="Degrees", ac=True, value=str(gl))
Gb = vp.Param(name="gb", ucd="pos.galactic.lat", unit="Degrees", ac=True, value=str(gb))
# v.What.append(vp.Group(params=[DM, Width, SNR, Flux, Gl, Gb], name="event parameters"))
v.What.append(vp.Group(params=[DM, DM_err, Width, SNR, Flux, Gl, Gb], name="event parameters"))
# Advanced parameters (note, change script if using a differeing MW model)
mw_dm = vp.Param(name="MW_dm_limit", unit="pc/cm^3", ac=True, value=str(ymw16))
mw_model = vp.Param(name="galactic_electron_model", value="YMW16")
redshift_inferred = vp.Param(name="redshift_inferred", ucd="src.redshift", unit="None", value=str(z))
redshift_inferred.Description = "Redshift estimated using z = DM/1000.0"
v.What.append(vp.Group(params=[mw_dm, mw_model, redshift_inferred], name="advanced parameters"))
# WhereWhen
vp.add_where_when(v, coords=vp.Position2D(ra=ra, dec=dec, err=errDeg, units='deg',
system=vp.definitions.sky_coord_system.utc_fk5_geo),
obs_time=datetime.datetime(utc_YY, utc_MM, utc_DD, utc_hh, utc_mm, int(utc_ss),
tzinfo=pytz.UTC),
observatory_location="WSRT")
# Why
vp.add_why(v, importance=importance)
v.Why.Name = name
if vp.valid_as_v2_0(v):
with open('{}.xml'.format(utc), 'wb') as f:
voxml = vp.dumps(v)
xmlstr = minidom.parseString(voxml).toprettyxml(indent=" ")
f.write(xmlstr.encode())
self.logger.info(vp.prettystr(v.Who))
self.logger.info(vp.prettystr(v.What))
self.logger.info(vp.prettystr(v.WhereWhen))
self.logger.info(vp.prettystr(v.Why))
else:
self.logger.error("Unable to write file {}.xml".format(name))
