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quakeml.py
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quakeml.py
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#####################################
# Convert quakeml catalogs to pandas
# and vice versa
import pandas
import lxml.etree as le
#TODO: publicID in quakeml should refer to webservice address
#TODO: add second nodal plane!?
def event2utc(event):
'''
given event returns UTC string
'''
d=event.fillna(0)
return '{:04d}-{:02d}-{:02d}T{:02d}:{:02d}:{:09f}Z'.format(int(d.year),int(max(d.month,1)),int(max(d.day,1)),int(d.hour),int(d.minute),d.second)
def utc2event(utc):
'''
given utc string returns list with year,month,day,hour,minute,second
'''
#last part usually either Z(ulu) or UTC, if not fails
if utc[-3:]=='UTC':
utc=utc[:-2]
elif utc[-1:]=='Z':
pass
else:
raise Exception('Cannot handle timezone other than Z(ulu) or UTC: {}'.format(utc))
date,time = utc.split('T')
return [int(v) if i<5 else float(v) for i,v in enumerate([int(d) for d in date.split('-')]+[float(t) for t in time[:-1].split(':')])]
def add_uncertain_child(parent,childname,value,uncertainty):
'''
Adds an uncertain child with value/uncertainty pair
'''
child = le.SubElement(parent,childname)
v = le.SubElement(child,'value')
v.text = str(value)
u = le.SubElement(child,'uncertainty')
u.text = str(uncertainty)
return parent
def events2quakeml(catalog,provider='GFZ'):
'''
Given a pandas dataframe with events returns QuakeML version of
the catalog
'''
xml_namespace = 'http://quakeml.org/xmlns/quakeml/1.2'
quakeml = le.Element('eventParameters',namespace=xml_namespace)
#go through all events
for i in range(len(catalog)):
quake = catalog.iloc[i]
event = le.SubElement(quakeml,'event',{'publicID':str(quake.eventID)})
preferredOriginID = le.SubElement(event,'preferredOriginID')
preferredOriginID.text=str(quake.eventID)
preferredMagnitudeID = le.SubElement(event,'preferredMagnitudeID')
preferredMagnitudeID.text=str(quake.eventID)
qtype = le.SubElement(event,'type')
qtype.text = 'earthquake'
description = le.SubElement(event,'description')
text = le.SubElement(description,'text')
text.text = str(quake.type)
#origin
origin = le.SubElement(event,'origin',{'publicID':str(quake.eventID)})
origin = add_uncertain_child(origin,childname='time',value=event2utc(quake),uncertainty=str(quake.timeUncertainty))
#time = le.SubElement(origin,'time')
#value = le.SubElement(time,'value')
#value.text = event2utc(quake)
#uncertainty = le.SubElement(time,'uncertainty')
#uncertainty.text = str(quake.timeUncertainty)
origin = add_uncertain_child(origin,childname='latitude',value=str(quake.latitude),uncertainty=str(quake.latitudeUncertainty))
#latitude = le.SubElement(origin,'latitude')
#value = le.SubElement(latitude,'value')
#value.text = str(quake.latitude)
#uncertainty = le.SubElement(latitude,'uncertainty')
#uncertainty.text = str(quake.sigmaLatitude)
origin = add_uncertain_child(origin,childname='longitude',value=str(quake.longitude),uncertainty=str(quake.longitudeUncertainty))
#longitude = le.SubElement(origin,'longitude')
#value = le.SubElement(longitude,'value')
#value.text = str(quake.longitude)
#uncertainty = le.SubElement(longitude,'uncertainty')
#uncertainty.text = str(quake.sigmaLongitude)
origin = add_uncertain_child(origin,childname='depth',value=str(quake.depth),uncertainty=str(quake.depthUncertainty))
#depth = le.SubElement(origin,'depth')
#value = le.SubElement(depth,'value')
#value.text = str(quake.depth)
#uncertainty = le.SubElement(depth,'uncertainty')
#uncertainty.text = str(quake.depthUncertainty)
creationInfo = le.SubElement(origin,'creationInfo')
author = le.SubElement(creationInfo,'value')
author.text = provider
#originUncertainty
originUncertainty = le.SubElement(event,'originUncertainty')
#NOTE: imo this should be decided during processing and not on data level --> NOT included
#preferredDescription = le.SubElement(originUncertainty,'originUncertainty')
#preferredDescription.text = quake.preferredOriginUncertainty
horizontalUncertainty = le.SubElement(originUncertainty,'horizontalUncertainty')
horizontalUncertainty.text = str(quake.horizontalUncertainty)
minHorizontalUncertainty = le.SubElement(originUncertainty,'minHorizontalUncertainty')
minHorizontalUncertainty.text = str(quake.minHorizontalUncertainty)
maxHorizontalUncertainty = le.SubElement(originUncertainty,'maxHorizontalUncertainty')
maxHorizontalUncertainty.text = str(quake.maxHorizontalUncertainty)
azimuthMaxHorizontalUncertainty = le.SubElement(originUncertainty,'azimuthMaxHorizontalUncertainty')
azimuthMaxHorizontalUncertainty.text = str(quake.azimuthMaxHorizontalUncertainty)
#magnitude
magnitude = le.SubElement(event,'magnitude',{'publicID':str(quake.eventID)})
magnitude = add_uncertain_child(magnitude,childname='mag',value=str(quake.magnitude),uncertainty=str(quake.magnitudeUncertainty))
#mag = le.SubElement(magnitude,'mag')
#value = le.SubElement(mag,'value')
#value.text = str(quake.magnitude)
#uncertainty = le.SubElement(magnitude,'uncertainty')
#uncertainty.text = str(quake.magnitudeUncertainty)
mtype = le.SubElement(magnitude,'type')
mtype.text = 'MW'
creationInfo = le.SubElement(magnitude,'creationInfo')
author = le.SubElement(creationInfo,'value')
author.text = provider
#plane (write only fault plane not auxilliary)
focalMechanism = le.SubElement(event,'focalMechanism',{'publicID':str(quake.eventID)})
nodalPlanes = le.SubElement(focalMechanism,'nodalPlanes')
nodalPlane1 = le.SubElement(nodalPlanes,'nodalPlane1')
nodalPlane1 = add_uncertain_child(nodalPlane1,childname='strike',value=str(quake.strike),uncertainty=str(quake.strikeUncertainty))
#strike = le.SubElement(nodalPlane1,'strike')
#value = le.SubElement(strike,'value')
#value.text = str(quake.strike)
#uncertainty = le.SubElement(strike,'uncertainty')
#uncertainty.text = str(quake.sigmaStrike)
nodalPlane1 = add_uncertain_child(nodalPlane1,childname='dip',value=str(quake.dip),uncertainty=str(quake.dipUncertainty))
#dip = le.SubElement(nodalPlane1,'dip')
#value = le.SubElement(dip,'value')
#value.text = str(quake.dip)
#uncertainty = le.SubElement(dip,'uncertainty')
#uncertainty.text = str(quake.sigmaDip)
nodalPlane1 = add_uncertain_child(nodalPlane1,childname='rake',value=str(quake.rake),uncertainty=str(quake.rakeUncertainty))
#rake = le.SubElement(nodalPlane1,'rake')
#value = le.SubElement(rake,'value')
#value.text = str(quake.rake)
#uncertainty = le.SubElement(rake,'uncertainty')
#uncertainty.text = str(quake.sigmaRake)
preferredPlane = le.SubElement(nodalPlanes,'preferredPlane')
preferredPlane.text = 'nodalPlane1'
#return str(le.tostring(quakeml,pretty_print=True,xml_declaration=True),encoding='utf-8')
return le.tostring(quakeml,pretty_print=True,encoding='unicode')
def get_uncertain_child(parent,childname):
'''
Given a childname returns value and uncertainty
'''
try:
value = float(parent.find(childname).findtext('value'))
except:
value = float('NAN')
try:
uncertainty = float(parent.find(childname).findtext('uncertainty'))
except:
uncertainty = float('NAN')
return [value,uncertainty]
def quakeml2events(quakemlfile,provider='GFZ'):
'''
Given a quakeml file/or string returns a pandas dataframe
'''
#TODO: add uncertainty
try:
#read quakeml catalog
with open(quakemlfile,'r') as f:
quakeml = f.read()
except:
#maybe already string
quakeml = quakemlfile
quakeml = le.fromstring(quakeml)
#initialize catalog
index = [i for i in range(len(quakeml))]
columns=['eventID', 'Agency', 'Identifier', 'year', 'month', 'day', 'hour', 'minute', 'second', 'timeUncertainty', 'longitude', 'longitudeUncertainty', 'latitude', 'latitudeUncertainty','horizontalUncertainty','maxHorizontalUncertainty', 'minHorizontalUncertainty', 'azimuthMaxHorizontalUncertainty', 'depth', 'depthUncertainty', 'magnitude', 'magnitudeUncertainty','rake','rakeUncertainty','dip','dipUncertainty','strike','strikeUncertainty','type', 'probability']
catalog=pandas.DataFrame(index=index,columns=columns)
#add individual events to catalog
for i,event in enumerate(quakeml):
#get ID
catalog.iloc[i].eventID = event.attrib['publicID']
#type
catalog.iloc[i].type = event.find('description').findtext('text')
#origin
origin = event.find('origin')
#time
catalog.iloc[i].year,catalog.iloc[i].month,catalog.iloc[i].day,catalog.iloc[i].hour,catalog.iloc[i].minute,catalog.iloc[i].second = utc2event(origin.find('time').findtext('value'))
catalog.iloc[i].timeUncertainty = float(origin.find('time').findtext('uncertainty'))
#latitude/longitude/depth
catalog.iloc[i].latitude, catalog.iloc[i].latitudeUncertainty = get_uncertain_child(origin,'latitude')
catalog.iloc[i].longitude, catalog.iloc[i].longitudeUncertainty = get_uncertain_child(origin,'longitude')
catalog.iloc[i].depth, catalog.iloc[i].depthUncertainty = get_uncertain_child(origin,'depth')
#agency/provider
catalog.iloc[i].agency = origin.find('creationInfo').findtext('value')
#magnitude
magnitude = event.find('magnitude')
catalog.iloc[i].magnitude, catalog.iloc[i].magnitudeUncertainty = get_uncertain_child(magnitude,'mag')
#originUncertainty
originUncertainty = event.find('originUncertainty')
catalog.iloc[i].horizontalUncertainty = originUncertainty.find('horizontalUncertainty').findtext('value')
catalog.iloc[i].minHorizontalUncertainty = originUncertainty.find('minHorizontalUncertainty').findtext('value')
catalog.iloc[i].maxHorizontalUncertainty = originUncertainty.find('maxHorizontalUncertainty').findtext('value')
catalog.iloc[i].horizontalUncertainty = originUncertainty.find('azimuthMaxHorizontalUncertainty').findtext('value')
#plane
nodalPlanes = event.find('focalMechanism').find('nodalPlanes')
preferredPlane = nodalPlanes.findtext('preferredPlane')
preferredPlane = nodalPlanes.find(preferredPlane)
#GET uncertain child!!
catalog.iloc[i].strike,catalog.iloc[i].strikeUncertainty =get_uncertain_child(preferredPlane,'strike')
catalog.iloc[i].dip ,catalog.iloc[i].dipUncertainty = get_uncertain_child(preferredPlane,'dip')
catalog.iloc[i].rake ,catalog.iloc[i].rakeUncertainty = get_uncertain_child(preferredPlane,'rake')
#catalog.iloc[i].strike = float(nodalPlanes.find(preferredPlane).find('strike').findtext('value'))
#catalog.iloc[i].dip = float(nodalPlanes.find(preferredPlane).find('dip').findtext('value'))
#catalog.iloc[i].rake = float(nodalPlanes.find(preferredPlane).find('rake').findtext('value'))
return catalog