Introduction to the IRISSeismic Package

Jonathan Callahan (jonathan@mazamascience.com), Mazama Science

Robert Casey (rob@iris.washington.edu), IRIS DMC

Mary Templeton (met@iris.washington.edu), IRIS DMC

2018-05-07

Introduction

The IRISSeismic package for seismic data analysis was developed by Mazama Science for the IRIS DMC (Incorporated Research Institutions for Seismology - Data Management Center). This development is part of the MUSTANG project for automated QC of seismic data.

The goal of this package is to make it easy to obtain and work with data from IRIS DMC web services. This introduction will demonstrate some of the core functionality of the IRISSeismic package and how it can be used in interactive sessions. Detailed information about object properties and function arguments can be found in the package documentation.

The core objects in this package, especially Trace and Stream objects, borrow heavily from concepts and features found in the Python ObsPy package. References to specific ObsPy classes can be found in the source code.

Getting Started

For those who are not used to working with R, the Using R series of blog posts offers tips on how to get started and includes links to other introductory documentation.

RStudio

Users of the IRISSeismic package are encouraged to first download and install the RStudio integrated development environment for R. Newcomers to R will find RStudio a much friendlier environment in which to work.

First Example

Once you have an R environment up and running, the first step is to load the IRISSeismic package. Then you can create a new IrisClient object that will be responsible for all subsequent communication with DMC provided web services.

library(IRISSeismic)
iris <- new("IrisClient")

In order to get data from one of the IRIS DMC web services we must specify all the information needed to create a webservice request: network, station, location, channel, starttime, endtime. Each unique combination of these elements is known as a SNCL. These elements are passed to the getDataselect() method of the IrisClient as a series of character strings except for the times which are of type POSIXct. The user is responsible for creating datetime objects of class POSIXct.

The first three commands in the following code chunk use the IrisClient object to communicate with web services and return a Stream object full of data from the IRIS DMC. The fourth line checks to see how many distinct chunks of seismic data exist. The last line passes this Stream object to a function that will plot the times at which this channel was collecting data.

starttime <- as.POSIXct("2002-04-20", tz="GMT")
endtime <- as.POSIXct("2002-04-21", tz="GMT")
st <- getDataselect(iris,"US","OXF","","BHZ",starttime,endtime)
length(st@traces)
## [1] 5
plotUpDownTimes(st, min_signal=1, min_gap=1)

This station had a few minor data dropouts, causing the data to be broken up into several separate signals that the IRISSeismic package stores in Trace objects.

We can get more information on the gaps between traces with the getGaps() function. The duration (secs) of gaps between traces is displayed along with the number of samples that were missed during the gap.

getGaps(st)
## $gaps
## [1]  0.0000 58.7750 57.0749 47.5750 52.1750  0.0000
## 
## $nsamples
## [1]    0 2351 2283 1903 2087    0

Next we can examine various statistics for each individual trace with the following parallel- functions.

parallelLength(st)
## [1]   10733  663953 2163653  308769  300267
parallelMax(st)
## [1]  1218  1356 38406  6139  1305
parallelSd(st)
## [1] 101.14186  97.03080 484.53911 135.00670  93.05572

It looks like the third trace, with a larger maximum and standard deviation, might have a signal. Metadata for this trace is stored in the stats slot of the Trace object.

tr <- st@traces[[3]]
tr@stats
## Seismic Trace TraceHeader 
##  Network:        US 
##  Station:        OXF 
##  Location:        
##  Channel:        BHZ 
##  Quality:        M 
##  calib:          1 
##  npts:           2163653 
##  sampling rate:  40 
##  delta:          0.025 
##  starttime:      2002-04-20 04:43:03 
##  endtime:        2002-04-20 19:44:34 
##  latitude:       34.5118 
##  longitude:      -89.4092 
##  elevation:      101 
##  depth:          0 
##  azimuth:        0 
##  dip:            -90 
##  processing:

Finally, we can look at the seismic signal with the plot method.

plot(tr)

This small seismic signal was recorded in Oxford, Mississippi and is from a quake that occurred in New York state

Note: By default, data are subsampled before plotting to greatly! improve plotting speed. You can sometimes improve the appearance of a plot by reducing the amount of subsampling used. The plot method accepts a subsampling parameter to specify this.

Understanding Stream and Trace objects

In order to work effectively with the IRISSeismic package you must first understand the structure of the new S4 objects it defines. The package documentation gives a full description of each object but we can also interrogate them using the slotNames() function.

slotNames(st)
## [1] "url"                "requestedStarttime" "requestedEndtime"  
## [4] "act_flags"          "io_flags"           "dq_flags"          
## [7] "timing_qual"        "traces"

The Stream object has the following slots (aka properties or attributes):

When in doubt about what a particular slot contains, it is always a good idea to ask what type of object it is.

class(st@url)
## [1] "character"
class(st@requestedStarttime)
## [1] "POSIXct" "POSIXt"
class(st@traces)
## [1] "list"

The next code chunk examines the first Trace in our Stream.

Note: R uses double square brackets, [[...]] to access list items.

slotNames(st@traces[[1]])
## [1] "id"                    "stats"                 "Sensor"               
## [4] "InstrumentSensitivity" "SensitivityFrequency"  "InputUnits"           
## [7] "data"

The Trace object has the following slots:

The TraceHeader metadata and the actual signal come from the dataselect webservice. The instrument metadata are obtained from the station webservice.

Be careful with times

Time stamps associated with seismic data should be given as “Universal” or “GMT” times. When specifying times to be used with methods of the IRISSeismic package you must be careful to specify the timezone as R assumes the local timezone by default.

Also, R assumes that datetime strings are formatted with a space separating date and time as opposed to the ISO 8601 ‘T’ separator. If an ISO 8601 character string is provided without specific formatting instructions, the time portion of the string will be lost without any warning! So it is very important to be careful and consistent if you write code that converts ASCII strings into times.

A few examples will demonstrate the issues:

as.POSIXct("2010-02-27", tz="GMT") # good
## [1] "2010-02-27 GMT"
as.POSIXct("2010-02-27 04:00:00", tz="GMT") # good
## [1] "2010-02-27 04:00:00 GMT"
as.POSIXct("2010-02-27T04:00:00", tz="GMT",
           format="%Y-%m-%dT%H:%M:%OS") # good
## [1] "2010-02-27 04:00:00 GMT"
as.POSIXct("2010-02-27") # BAD -- no timezone
## [1] "2010-02-27 PST"
as.POSIXct("2010-02-27T04:00:00", tz="GMT") # BAD -- no formatting
## [1] "2010-02-27 GMT"

Example Operations

The example at the beginning of this vignette already demonstrated how to obtain seismic data from DMC web services, how to learn about the number and size of individual traces within the requested time range and how to generate a first plot of the seismic signal. This section will introduce more use cases that delve further into the capabilities of the IRISSeismic package. For complete details on available functions, please see the package documentation.

help("IRISSeismic",package="IRISSeismic")

Closer examination of a seismic signal

Once seismic data are in memory, performing mathematical analysis on those data can be very fast. All mathematical operations are performed on every data point.
But plotting can still be a slow process.

Note: The plot() method of Stream objects deals with gaps by first calling mergeTraces() to fill all gaps with missing values (NA). Then the single, merged trace is plotted with the plot() method for Trace objects. Any gaps of a significant size will be now visible in the resulting plot.

By default, the plot() method of Trace and Stream objects subsamples the data so that approximately 5,000 points are used in the plot. This dramatically speeds up plotting. One of the first things you will want to do with a full day’s worth of seismic signal is clip it to a region of interest. One way to do that would be to modify the starttime and endtime parameters to getDataselect and then make a data request covering a shorter period of time. A simpler technique, if the signal is already in memory, is to use the slice() method.

starttime <- as.POSIXct("2010-02-27", tz="GMT")
endtime <- as.POSIXct("2010-02-28", tz="GMT")
st <- getDataselect(iris,"IU","ANMO","00","BHZ",starttime,endtime)

start2 <- as.POSIXct("2010-02-27 06:40:00", tz="GMT")
end2 <- as.POSIXct("2010-02-27 07:40:00", tz="GMT")

tr1 <- st@traces[[1]]
tr2 <- slice(tr1, start2, end2)

layout(matrix(seq(2)))        # layout a 2x1 matrix
plot(tr1)
plot(tr2)

layout(1)                     # restore original layout

Detecting events with STA/LTA

Access to triggering algorithms for detecting events is provided by the STALTA() method of Trace objects. ( cf A Comparison of Select Trigger Algorithms for Automated Global Seismic Phase and Event Detection). The STALTA() method has the following arguments and defaults:

The STALTA() method returns a picker, a vector of numeric values, one for every value in the Trace@data slot. Note that this is a fairly compute-intensive operation. This picker can then be used with the triggerOnset() function to return the approximate start of the seismic signal.

We’ll test this with our original seismic signal.

starttime <- as.POSIXct("2002-04-20", tz="GMT")
endtime <- as.POSIXct("2002-04-21", tz="GMT")
st <- getDataselect(iris,"US","OXF","","BHZ",starttime,endtime)
tr <- st@traces[[3]]
picker <- STALTA(tr,3,30)
threshold <- quantile(picker,0.99999,na.rm=TRUE)
to <- triggerOnset(tr,picker,threshold)

NOTE: The STALTA() method is intended to be used for crude, automatic event detection, not precise determination of signal arrival. Optimal values for the arguments to the STALTA() method will depend on the details of the seismic signal.

The eventWindow() method allows you to focus on the region identified by the picker by automatically finding the trigger onset time and then slicing out the region of the trace centered on that time. This method has the following arguments and defaults:

layout(matrix(seq(3)))        # layout a 3x1 matrix
closeup1 <- eventWindow(tr,picker,threshold,3600)
closeup2 <- eventWindow(tr,picker,threshold,600)
plot(tr)
abline(v=to, col='red', lwd=2)
plot(closeup1)
abline(v=to, col='red', lwd=2)
plot(closeup2)
abline(v=to, col='red', lwd=2)

layout(1)                     # restore original layout

Data availability

The IrisClient also provides functionality for interacting with other web services at the DMC. The getAvailability() method allows users to query what SNCLs are available, obtaining that information from the station webservice.

Information is returned as a dataframe containing all the information returned by ws-availability. Standard DMC webservice wildcards can be used as in the example below which tells us what other ‘B’ channels are available at our station of interest during the time of the big quake above.

starttime <- as.POSIXct("2010-02-27", tz="GMT")
endtime <- as.POSIXct("2010-02-28", tz="GMT")
availability <- getAvailability(iris,"IU","ANMO","*","B??",starttime,endtime)
availability
##   network station location channel latitude longitude elevation depth
## 1      IU    ANMO       00     BH1 34.94598 -106.4571    1671.0 145.0
## 2      IU    ANMO       00     BH2 34.94598 -106.4571    1671.0 145.0
## 3      IU    ANMO       00     BHZ 34.94598 -106.4571    1671.0 145.0
## 4      IU    ANMO       10     BH1 34.94591 -106.4571    1767.2  48.8
## 5      IU    ANMO       10     BH2 34.94591 -106.4571    1767.2  48.8
## 6      IU    ANMO       10     BHZ 34.94591 -106.4571    1767.2  48.8
##   azimuth dip                            instrument       scale scalefreq
## 1     328   0 Geotech KS-54000 Borehole Seismometer  3456610050      0.02
## 2      58   0 Geotech KS-54000 Borehole Seismometer  3344369920      0.02
## 3       0 -90 Geotech KS-54000 Borehole Seismometer  3275079940      0.02
## 4      64   0  Guralp CMG3-T Seismometer (borehole) 32805599200      0.02
## 5     154   0  Guralp CMG3-T Seismometer (borehole) 32654999600      0.02
## 6       0 -90  Guralp CMG3-T Seismometer (borehole) 33067200500      0.02
##   scaleunits samplerate           starttime             endtime
## 1        M/S         20 2008-06-30 20:00:00 2011-02-18 19:11:00
## 2        M/S         20 2008-06-30 20:00:00 2011-02-18 19:11:00
## 3        M/S         20 2008-06-30 20:00:00 2011-02-18 19:11:00
## 4        M/S         40 2008-06-30 20:00:00 2011-02-19 06:53:00
## 5        M/S         40 2008-06-30 20:00:00 2011-02-19 06:53:00
## 6        M/S         40 2008-06-30 20:00:00 2011-02-19 06:53:00
##           snclId
## 1 IU.ANMO.00.BH1
## 2 IU.ANMO.00.BH2
## 3 IU.ANMO.00.BHZ
## 4 IU.ANMO.10.BH1
## 5 IU.ANMO.10.BH2
## 6 IU.ANMO.10.BHZ

The getAvailability() method accepts the following arguments:

Other IRIS DMC web services

Several methods of the IrisClient class work very similarly to the getAvailability() method in that they return dataframes of information obtained from web services of the same name. The suite of methods returning dataframes includes:

The following example demonstrates the use of several of these services together to do the following:

  1. find seismic events on a particular day
  2. find available US network BHZ channels in the hour after the biggest event that day
  3. determine the easternmost of those channels
  4. get the P and S travel times to that station
  5. plot the seismic signal detected at that station with markers for P and S arrival times
# Open a connection to IRIS DMC webservices
iris <- new("IrisClient")

# Two days around the "Nisqually Quake"
starttime <- as.POSIXct("2001-02-27", tz="GMT")
endtime <- starttime + 3600 * 24 *2

# Find biggest seismic event over these two days -- it's the "Nisqually"
events <- getEvent(iris, starttime, endtime, minmag=5.0)
bigOneIndex <- which(events$magnitude == max(events$magnitude))
bigOne <- events[bigOneIndex[1],]

# Find US stations that are available within 10 degrees of arc of the 
# event location during the 15 minutes after the event
start <- bigOne$time
end <- start + 900
av <- getAvailability(iris, "US", "", "", "BHZ", start, end,
                      latitude=bigOne$latitude, longitude=bigOne$longitude,
                      minradius=0, maxradius=10)
    
# Get the station the furthest East
minLonIndex <- which(av$longitude == max(av$longitude))
snclE <- av[minLonIndex,]

# Get travel times to this station
traveltimes <- getTraveltime(iris, bigOne$latitude, bigOne$longitude, bigOne$depth,
                             snclE$latitude, snclE$longitude)

# Look at the list                             
traveltimes
##   distance depth phaseName travelTime rayParam takeoff incident
## 1     8.95  51.8         P     126.63   13.686   86.32    45.55
## 2     8.95  51.8         S     226.82   24.532   84.61    47.84
## 3     8.95  51.8       PcP     507.27    0.855    3.57     2.55
## 4     8.95  51.8       ScS     928.95    1.576    3.67     2.73
## 5     8.95  51.8     PKiKP     987.62    0.200    0.84     0.60
## 6     8.95  51.8     SKiKS    1406.16    0.224    0.52     0.39
##   puristDistance puristName
## 1           8.95          P
## 2           8.95          S
## 3           8.95        PcP
## 4           8.95        ScS
## 5           8.95      PKiKP
## 6           8.95      SKiKS
# Find the P and S arrival times
pArrival <- start + traveltimes$travelTime[traveltimes$phaseName=="P"]
sArrival <- start + traveltimes$travelTime[traveltimes$phaseName=="S"] 

# Get the BHZ signal for this station
st <- getDataselect(iris,snclE$network,snclE$station,
                    snclE$location,snclE$channel,
                    start,end)

# Check that there is only a single trace
length(st@traces)
## [1] 1
# Plot the seismic trace and mark the "P" and "S" arrival times
tr <- st@traces[[1]]
plot(tr, subsampling=1) # need subsampling=1 to add vertical lines with abline()
abline(v=pArrival, col='red')
abline(v=sArrival, col='blue')