def send(self):
#is it possible to send a directory and a file in the same command?
#let's assume it isn't
if self.filesToSend is not None and self.directoryToSend is not None:
raise SenderError('For PDL, you must choose files OR a directory to send, not both')
for prop in self.required_properties:
if prop not in self.properties.keys():
raise SenderError('"%s" property must be supplied to send via PDL')
jarfile = self.properties['jarfile']
source = self.properties['source']
ptype = self.properties['type']
keyfile = self.properties['keyfile']
configfile = self.properties['configfile']
code = self.properties['code']
if not os.path.isfile(jarfile):
raise SenderError('Could not find Java jar file "%s".' % jarfile)
if not os.path.isfile(configfile):
raise SenderError('Could not find PDL config file "%s".' % configfile)
if not os.path.isfile(keyfile):
raise SenderError('Could not find PDL private key file "%s".' % keyfile)
#build pdl command line from properties
javabin = self.findjava()
if javabin is None:
raise SenderError('Could not find Java binary on system path.')
basecmd = '%s -jar %s --send --source=%s --type=%s --privateKey=%s --configFile=%s --code=%s ' % (javabin,jarfile,source,ptype,keyfile,configfile,code)
nuggets = []
for key,value in self.properties.iteritems():
if key in self.required_properties:
continue
if isinstance(value,int):
vstr = '%i' % value
elif isinstance(value,float):
vstr = '%f' % value
else:
vstr = value
nuggets.append('--%s=%s' % (key,vstr))
cmd = basecmd + ' '.join(nuggets) + ' '
nfiles = 0
#pdl can be used to send information without sending any files
if self.directoryToSend is None and self.filesToSend is None:
#this is ok - PDL products can be defined completely on the command line
retcode,stdout,stderr = getCommandOutput(cmd)
if not retcode:
raise SenderError('Could not send directory "%s" due to error "%s"' % (self.directoryToSend,stdout+stderr))
if self.directoryToSend is not None:
cmd = cmd + '--directory=%s ' % self.directoryToSend
retcode,stdout,stderr = getCommandOutput(cmd)
if not retcode:
raise SenderError('Could not send directory "%s" due to error "%s"' % (self.directoryToSend,stdout+stderr))
nfiles += len(os.walk(self.directoryToSend).next()[2])
elif self.filesToSend is not None:
for f in self.filesToSend:
cmd = cmd + '--file=%s ' % f
retcode,stdout,stderr = getCommandOutput(cmd)
if not retcode:
raise SenderError('PDL command: "%s"\nCould not send file "%s" due to error "%s"' % (cmd,f,stdout+stderr))
nfiles += 1
return nfiles
def runSecondary(url,thisdir):
cmd = os.path.join(thisdir,SECHAZ)
cmd += ' -r %s' % url
retcode,stdout,stderr = getCommandOutput(cmd)
pdf = None
png = None
for line in stdout.split('\n'):
if line.find('Saving map output') > -1:
parts = line.split()
tfile = parts[-1]
if tfile.find('pdf') > -1:
pdf = tfile
if tfile.find('png') > -1:
png = tfile
return (pdf,png)
def send(self):
#we can really only support sending of one file and/or one directory, so error out
#if someone has specified more than one of either.
if len(self.files) > 1:
raise ShakeMapException(
'For PDL, you may only send one file at a time.')
if len(self.directories) > 1:
raise ShakeMapException(
'For PDL, you may only send one directory at a time.')
#make sure we have all the required properties
for prop in self.required_properties:
if prop not in list(self.properties.keys()):
raise ShakeMapException(
'"%s" property must be supplied to send via PDL')
#build pdl command line from properties
self.properties['command'] = 'send'
self.properties['status'] = 'UPDATE'
if self.files:
self.properties['file'] = self.files[0]
else:
self.properties['file'] = ''
if self.directories:
self.properties['directory'] = self.directories[0]
else:
self.properties['directory'] = ''
cmd = self.pdlcmd
for propkey, propvalue in self.properties.items():
cmd = cmd.replace('[' + propkey.upper() + ']', propvalue)
#call PDL on the command line
retcode, stdout, stderr = getCommandOutput(cmd)
if not retcode:
fmt = 'Could not send product "%s" due to error "%s"'
tpl = (code, stdout + stderr)
raise ShakeMapException(fmt % tpl)
#return the number of files we just sent
nfiles = 0
if self.properties['file']:
nfiles += 1
if self.properties['directory']:
nfiles += len(os.listdir(self.properties['directory']))
return nfiles
def delete(self):
for prop in self.required_properties:
if prop not in list(self.properties.keys()):
raise ShakeMapException(
'"%s" property must be supplied to send via PDL')
#build pdl command line from properties
self.properties['status'] = 'DELETE'
self.properties['files'] = ''
self.properties['directories'] = ''
cmd = self.pdlcmd
for propkey, propvalue in self.properties.items():
cmd = cmd.replace('[' + propkey.upper() + ']', propvalue)
retcode, stdout, stderr = getCommandOutput(cmd)
if not retcode:
fmt = 'Could not delete product "%s" due to error "%s"'
tpl = (code, stdout + stderr)
raise ShakeMapException(fmt % tpl)
def main(args):
globaldict = getGlobalConfig()
shakehome = globaldict['shakehome']
popfile = globaldict['popfile']
if shakehome is None:
print 'Cannot find ShakeMap home folder on this system.'
sys.exit(1)
datadir = os.path.join(shakehome,'data',args.event)
if not os.path.isdir(datadir):
print 'Cannot find event %s on the system' % args.event
sys.exit(1)
#Make sure the timeoutput folder is there (can't put our time grids in output - that gets
#wiped out every time shakemap runs
outfolder = os.path.join(datadir,'timeoutput')
if not os.path.isdir(outfolder):
os.makedirs(outfolder)
#now look for config file in top-level folder
configfile = os.path.join(datadir,'alert.conf')
if not os.path.isfile(configfile):
print 'Cannot find alert config file for %s in the data directory' % args.event
sys.exit(1)
config = ConfigParser.ConfigParser()
config.readfp(open(configfile))
#get the bounds of the map so we can find cities
xmin = float(config.get('MAP','xmin'))
xmax = float(config.get('MAP','xmax'))
ymin = float(config.get('MAP','ymin'))
ymax = float(config.get('MAP','ymax'))
citylist = getCityList(xmin,xmax,ymin,ymax,globaldict['cityfile'])
#Get the MMI threshold below which alert times will NOT be saved
mmithresh = float(config.get('MAP','mmithresh'))
#get the array of epicenters
lats = [float(p) for p in config.get('FAULT','lats').split()]
lons = [float(p) for p in config.get('FAULT','lons').split()]
#write out a new grind.conf file
writeGrind(config,datadir)
#instantiate our p/s travel time calculator
calc = TravelTimeCalculator()
#where is the grind binary?
grindbin = os.path.join(shakehome,'bin','grind')
#specify the event.xml file, get the depth of the event
eventfile = os.path.join(datadir,'input','event.xml')
root = parse(eventfile)
eq = root.getElementsByTagName('earthquake')[0]
depth = float(eq.getAttribute('depth'))
root.unlink()
#get the dimensionality of the grid file and of the pop grid we'll interpolate to
gridfile = os.path.join(datadir,'output','grid.xml')
if not os.path.isfile(gridfile):
grindcmd = '%s -event %s' % (grindbin,args.event)
res,stdout,stderr = getCommandOutput(grindcmd)
mmigrid = ShakeGrid(gridfile,variable='MMI')
popgrid = EsriGrid(popfile)
popgrid.load(bounds=mmigrid.getRange())
m,n = popgrid.griddata.shape
#loop over all the event realizations
timefiles = []
timestack = np.zeros((m,n,len(lats)),dtype=np.float32)
for i in range(0,len(lats)):
print 'Calculating arrival times for scenario %i of %i' % (i+1,len(lats))
lat = lats[i]
lon = lons[i]
if i == 0:
lonoff = 0
latoff = 0
else:
lonoff = -1* (lons[i] - lons[i-1])
latoff = lats[i] - lats[i-1]
#modify the event.xml file to have the new lat/lon epicenter
sourcetext = getEventText(eventfile,lat,lon)
f = open(eventfile,'wt')
f.write(sourcetext)
f.close()
sdict = getSlowestStation(lat,lon,depth,calc)
ptime = sdict['time']
stationlat = sdict['lat']
stationlon = sdict['lon']
grindcmd = '%s -latoff %f -lonoff %f -event %s' % (grindbin,latoff,lonoff,args.event)
res,stdout,stderr = getCommandOutput(grindcmd)
if not res:
print 'Grind command failed: "%s", "%s"' % (stdout,stderr)
sys.exit(1)
#Get the grid.xml output, do some time calculations
mmigrid = ShakeGrid(gridfile,variable='MMI')
timegrid = np.zeros((m,n),dtype=np.float32)
for row in range(0,m):
for col in range(0,n):
mmilat,mmilon = mmigrid.getLatLon(row,col)
distance = locations2degrees(lat,lon,mmilat,mmilon)
tmp,stime = calc.getTravelTimes(distance,depth)
timegrid[row,col] = stime - ptime
#debugging
f = plt.figure()
plt.subplot(2,1,1)
plt.imshow(mmigrid.griddata)
plt.colorbar()
plt.subplot(2,1,2)
plt.imshow(timegrid)
plt.colorbar()
plt.savefig(os.path.join(outfolder,'timegrid.png'))
plt.close(f)
with warnings.catch_warnings():
warnings.simplefilter("ignore")
exposure,timegrid = getTimeExposure(timegrid,mmigrid,popfile,mmithresh)
print 'Population Warning Times for epicenter %.4f,%.4f' % (lat,lon)
printExposure(exposure)
expofile = os.path.join(outfolder,'expo%03i.json' % (i+1))
f = open(expofile,'wt')
f.write(json.dumps(exposure))
f.close()
timefile = os.path.join(outfolder,'timegrid%03i.flt' % (i+1))
timefiles.append(timefile)
metadict = {'epilat':lat,'epilon':lon,'eventid':args.event}
saveTimeGrid(timefile,timegrid,mmigrid.geodict,metadict)
timestack[:,:,i] = timegrid
alertgrid = popgrid
alertgrid.griddata = timegrid
makeMap(alertgrid,'alertmap_%i' % i,outfolder,popfile,globaldict['popcolormap'],sdict,citylist,[lat],[lon])
methods = config.get('MAP','output').split(',')
for method in methods:
if method == 'median':
statgrid = np.median(timestack,axis=2)
if method == 'mean':
statgrid = np.nanmean(timestack,axis=2)
if method == 'min':
statgrid = np.nanmin(timestack,axis=2)
if method == 'max':
statgrid = np.nanmax(timestack,axis=2)
timegrid = popgrid
timegrid.griddata = statgrid
makeMap(timegrid,method,outfolder,popfile,globaldict['popcolormap'],sdict,citylist,lats,lons)
def send(self):
#is it possible to send a directory and a file in the same command?
#let's assume it isn't
if self.filesToSend is not None and self.directoryToSend is not None:
raise SenderError(
'For PDL, you must choose files OR a directory to send, not both'
)
for prop in self.required_properties:
if prop not in self.properties.keys():
raise SenderError(
'"%s" property must be supplied to send via PDL')
jarfile = self.properties['jarfile']
source = self.properties['source']
ptype = self.properties['type']
keyfile = self.properties['keyfile']
configfile = self.properties['configfile']
code = self.properties['code']
if not os.path.isfile(jarfile):
raise SenderError('Could not find Java jar file "%s".' % jarfile)
if not os.path.isfile(configfile):
raise SenderError('Could not find PDL config file "%s".' %
configfile)
if not os.path.isfile(keyfile):
raise SenderError('Could not find PDL private key file "%s".' %
keyfile)
#build pdl command line from properties
javabin = self.findjava()
if javabin is None:
raise SenderError('Could not find Java binary on system path.')
basecmd = '%s -jar %s --send --source=%s --type=%s --privateKey=%s --configFile=%s --code=%s ' % (
javabin, jarfile, source, ptype, keyfile, configfile, code)
nuggets = []
for key, value in self.properties.iteritems():
if key in self.required_properties:
continue
if isinstance(value, int):
vstr = '%i' % value
elif isinstance(value, float):
vstr = '%f' % value
else:
vstr = value
nuggets.append('--%s=%s' % (key, vstr))
cmd = basecmd + ' '.join(nuggets) + ' '
nfiles = 0
#pdl can be used to send information without sending any files
if self.directoryToSend is None and self.filesToSend is None:
#this is ok - PDL products can be defined completely on the command line
retcode, stdout, stderr = getCommandOutput(cmd)
if not retcode:
raise SenderError(
'Could not send directory "%s" due to error "%s"' %
(self.directoryToSend, stdout + stderr))
if self.directoryToSend is not None:
cmd = cmd + '--directory=%s ' % self.directoryToSend
retcode, stdout, stderr = getCommandOutput(cmd)
if not retcode:
raise SenderError(
'Could not send directory "%s" due to error "%s"' %
(self.directoryToSend, stdout + stderr))
nfiles += len(os.walk(self.directoryToSend).next()[2])
elif self.filesToSend is not None:
for f in self.filesToSend:
cmd = cmd + '--file=%s ' % f
retcode, stdout, stderr = getCommandOutput(cmd)
if not retcode:
raise SenderError(
'PDL command: "%s"\nCould not send file "%s" due to error "%s"'
% (cmd, f, stdout + stderr))
nfiles += 1
return nfiles
if __name__ == '__main__':
#make a data set
data = np.arange(0,16).reshape(4,4).astype(np.int32)
geodict = {'xmin':0.5,'xmax':3.5,'ymin':0.5,'ymax':3.5,'xdim':1.0,'ydim':1.0,'nrows':4,'ncols':4}
gmtgrid = GMTGrid(data,geodict)
#save that data set to a grid
gmtgrid.save('gmt_from_python.grd')
#use gmt to get the value at 1.5,1.5 (should be 9)
f = open('track.xy','wt')
f.write('1.5 1.5\n')
f.close()
cmd = 'gmt grdtrack -nn track.xy -Ggmt_from_python.grd'
res,stdout,stderr = getCommandOutput(cmd)
print stdout
#now create an XY file from our grid
f = open('from_python.xyz','wt')
for i in range(0,geodict['nrows']):
for j in range(0,geodict['ncols']):
lat,lon = gmtgrid.getLatLon(i,j)
value = gmtgrid.getValue(lat,lon)
f.write('%.1f %.1f %i\n' % (lon,lat,value))
f.close()
#now create a grid file from our XY file
cmd = 'gmt xyz2grd -R0.5/3.5/0.5/3.5 -I1.0/1.0 from_python.xyz -Gfrom_gmt.grd'
res,stdout,stderr = getCommandOutput(cmd)
def main(args):
eventid = args.id
radius = args.radius
#does the bayesloc folder exist?
if not os.path.isdir(BAYESDIR):
print FOLDER_ERROR
sys.exit(1)
bayesbin = os.path.join(BAYESDIR,'bin',BAYESBIN)
ttimes = glob.glob(os.path.join(BAYESDIR,'ttimes','ak135.*'))
if not os.path.isfile(bayesbin):
print FOLDER_ERROR
sys.exit(1)
if not len(ttimes):
print FOLDER_ERROR
sys.exit(1)
bayesdb = os.path.join(BAYESDIR,BAYESDB)
# if startOver and os.path.isfile(bayesdb):
# os.remove(bayesdb)
#does the database exist - if not, create it
if not os.path.isfile(bayesdb):
db = sqlite3.connect(bayesdb)
cursor = db.cursor()
createTables(db,cursor)
else:
db = sqlite3.connect(bayesdb)
cursor = db.cursor()
#Delete selected list of events
if args.delete:
nevents = deleteEvents(db,cursor,args.delete)
print '%i events deleted from the database.' % nevents
sys.exit(0)
#Return some stats about the current database
if args.stats:
nevents,nstations,narrivals = getStats(cursor)
print 'Your database contains information about:'
print '\t%i events' % nevents
print '\t%i stations' % nstations
print '\t%i picks' % narrivals
sys.exit(0)
eventinfo = getPhaseData(eventid=eventid)
if not len(eventinfo):
print 'Could not find event %s in ComCat. Returning.'
sys.exit(1)
#get the information about the input event
eventinfo = eventinfo[0]
eventlat = eventinfo.origins[0]['lat']
eventlon = eventinfo.origins[0]['lon']
eventtime = eventinfo.origins[0]['time']
if eventtime < args.begindate or eventtime > args.enddate:
fmt = 'Event %s (%s) is outside the time bounds you specified. %s to %s. Exiting.'
print fmt % (eventinfo.eventcode,eventtime,args.begindate,args.enddate)
sys.exit(1)
tnow = datetime.utcnow()
eventfolder = os.path.join(BAYESDIR,'events',eventid)
if not os.path.isdir(eventfolder):
os.makedirs(eventfolder)
# eventlist1 = getEventData(radius=(eventlat,eventlon,0,radius),
# starttime=args.begindate,
# endtime=args.enddate,catalog='pde')
eventlist = getEventData(radius=(eventlat,eventlon,0,radius),
starttime=args.begindate,
endtime=args.enddate,catalog='us')
#eventlist = eventlist1 + eventlist2
if args.count:
fmt = 'There are %i events inside %.1f km radius around event %s (%.4f,%.4f)'
print fmt % (len(eventlist),radius,eventid,eventlat,eventlon)
sys.exit(0)
#check to see if event has already been located - if so, stop, unless we're being forced
if not args.force:
sql = 'SELECT id,code,rlat,rlon,rdepth,rtime FROM event WHERE code="%s"' % eventid
cursor.execute(sql)
row = cursor.fetchone()
if row is not None and row[2] is not None:
print 'Event %s is already in the database. Stopping.' % eventid
sys.exit(0)
priors = getEventPriors(eventlist,cursor)
stations,arrivals,newevents = getProcessedData(eventlist,db,cursor,ndays=NWEEKS*7)
fmt = 'In database: %i stations, %i arrivals. %i events not in db.'
#print fmt % (len(stations),len(arrivals),len(newevents))
missing_stations = []
for event in newevents:
phasedata = getPhaseData(eventid=event)
if phasedata is None:
continue
if not len(phasedata[0].magnitudes):
continue
newstations,newarrivals,ms = insertPhaseData(phasedata[0],db,cursor)
stations = dict(stations.items() + newstations.items())
arrivals += newarrivals
missing_stations += ms
print 'After searching online:'
fmt = 'In database: %i stations, %i arrivals. %i missing stations.'
print fmt % (len(stations),len(arrivals),len(missing_stations))
stafile = 'station.dat'
stationfile = os.path.join(eventfolder,stafile)
f = open(stationfile,'wt')
f.write('sta_id lat lon elev\n')
for stationcode,stationvals in stations.iteritems():
slat,slon,elev = stationvals
f.write('%s %.4f %.4f %.3f\n' % (stationcode,slat,slon,elev))
f.close()
arrfile = 'arrival.dat'
arrivalfile = os.path.join(eventfolder,arrfile)
f = open(arrivalfile,'wt')
f.write('ev_id sta_id phase time\n')
for arrival in arrivals:
eid,scode,phase,time = arrival
f.write('%i %s %s %.3f\n' % (eid,scode,phase,time))
f.close()
prifile = 'prior.dat' #??
priorfile = os.path.join(eventfolder,prifile)
f = open(priorfile,'wt')
f.write('ev_id lat_mean lon_mean dist_sd depth_mean depth_sd time_mean time_sd\n')
for prior in priors:
evid,plat,plon,pdepth,ptime = prior
f.write('%i %.4f %.4f 0.0 %.1f 0.0 %.3f 0.0\n' % (evid,plat,plon,pdepth,ptime))
f.close()
#write the config file
configfile = os.path.join(eventfolder,'bayesloc.cfg')
config = CONFIG.replace('BAYESLOC',BAYESLOC)
config = config.replace('EVENTFOLDER',eventfolder)
fcfg = open(configfile,'wt')
fcfg.write(config)
fcfg.close()
#Run the BayesLoc program
#change to the eventfolder
cwd = os.getcwd()
os.chdir(eventfolder)
bayesbin = os.path.join(BAYESLOC,'bin','bayesloc')
cmd = '%s %s' % (bayesbin,configfile)
print 'Running command %s...' % cmd
t1 = datetime.now()
# process = subprocess.Popen(cmd, stdout=subprocess.PIPE)
# for c in iter(lambda: process.stdout.read(1), ''):
# sys.stderr.write(c)
res,stdout,stderr = getCommandOutput(cmd)
t2 = datetime.now()
if not res:
print 'BayesLoc command "%s" failed. \n%s\n%s.' % (cmd,stdout,stderr)
sys.exit(1)
else:
dt = ((t2-t1).seconds)/60.0
print 'BayesLoc command was successful - took %.1f minutes.' % dt
os.chdir(cwd)
resultfile = os.path.join(eventfolder,'output','origins_ned_stats.out')
f = open(resultfile,'rt')
f.readline()
eventlist = []
fieldlist = ['lat','lon','depth','time','rlat','rlon','rdepth','rtime','mag','nevents']
nevents = len(priors) + len(newevents)
for line in f.readlines():
parts = line.split()
eid = int(parts[0])
lat = float(parts[1])
lon = float(parts[2])
depth = float(parts[3])
time = UTCDateTime(float(parts[4])).datetime
efmt = 'UPDATE event set rlat=%.4f,rlon=%.4f,rdepth=%.1f,rtime="%s",nevents=%i WHERE id=%i'
equery = efmt % (lat,lon,depth,time,nevents,eid)
cursor.execute(equery)
db.commit()
query = 'SELECT %s FROM event WHERE id=%i' % (','.join(fieldlist),eid)
cursor.execute(query)
row = cursor.fetchone()
eventlist.append(dict(zip(fieldlist,row)))
f.close()
#make a map of all the relocated events
fname = makeMap(eventlist,eventlat,eventlon,eventfolder)
print 'Relocated events: %s' % fname
#tell the user what happened with the relocation
fmt = 'SELECT lat,lon,depth,time,rlat,rlon,rdepth,rtime,nevents FROM event WHERE code="%s"'
query = fmt % (eventid)
cursor.execute(query)
row = cursor.fetchone()
lat,lon,depth,time,rlat,rlon,rdepth,rtime,nevents = row
time = UTCDateTime(time).datetime
rtime = UTCDateTime(rtime).datetime
if rtime >= time:
dt = (rtime-time).seconds + ((rtime-time).microseconds)/float(1e6)
else:
dt = (time-rtime).seconds + ((time-rtime).microseconds)/float(1e6)
dd,az1,az2 = gps2DistAzimuth(lat,lon,rlat,rlon)
dd /= 1000.0
print 'Event %s was relocated using %i events.' % (eventid,nevents)
print 'Starting: %s (%.4f,%.4f) %.1f km' % (time.strftime('%Y-%m-%d %H:%M:%S'),lat,lon,depth)
print 'Relocated: %s (%.4f,%.4f) %.1f km' % (rtime.strftime('%Y-%m-%d %H:%M:%S'),rlat,rlon,rdepth)
print '%.1f km (%.1f degrees), %.1f seconds' % (dd,az1,dt)
cursor.close()
db.close()