FuncLab: MATLAB receiver function analysis
Contents
1. Updated April 17 2011 13 APPENDIX C DESCRIPTION OF SAC FILES SAC files for the receiver functions and seismograms may be produced in a variety of ways but regardless of the method of preprocessing some important formatting standards must be followed This appendix describes the format and headers needed in each of the files FuncLab imports 5 separate SAC files for a given calculated receiver function These include the vertical seismogram radial seismogram transverse seismogram radial receiver function and transverse receiver function It is preferred that all 5 files are time synched to the zero time of the receiver functions This makes plots in FuncLab make a lot more sense and prevents issues when interpreting the time axis Naming of the SAC files is an important first step All SAC files have a naming convention as follows STA_2 5 i 2z where STA is the station name 2 5 represents the Gaussian lowpass filter or any type of lowpass filter used i means that we used iterative deconvolution to calculate the receiver function and z is the seismogram component of motion The station name and the extension are the most important items of the name The extensions define the type of file as follows Z vertical seismogram radial seismogram t transverse seismogram eqr radial receiver function eqt transverse receiver function The SAC header definitions and descriptions for2. station longitude STEL 1 318000e 03 station elevation in meters STDP 0 000000e 00 station depth in meters EVLA 1 640000e 01 earthquake latitude EVLO 1 469000e 02 earthquake longitude EVEL 0 000000e 00 earthquake elevation in meters EVDP 5 300000e 04 earthquake depth in meters DIST 9 048033e 03 Updated April 17 2011 15 distance in kilometers from station to earthguake AZ 4 540545e 01 azimuth from earthquake to station BAZ 2 844766e 02 backazimuth from station to earthquake GCARC 8 138271e 01 distance in degrees from station to earthquake LOVROK TRUE set to TRUE to overwrite the file USER 3 028038e 02 predicted P wave ray parameter in sec rad USER8 0 000000e 00 predefines the trace edit status this is OPTIONAL but set to 0 if it is bad or 1 if it is good and you want to define it as an active RF NVHDR 6 header version number current version is 6 LPSPOL TRUE set to TRUE if component has positive polarity LCALDA TRUE set to TRUE if DIST AZ BAZ and GCARC are calculated from station earthquake coordinates KCMPNM BHZ component code should be set to BHZ for vertical BHR for radial and radial RFs and BHT for transverse and transverse RFs KNETWK TA network code MAG 5 500000e 00 earthquake body wave magnitude One note of caution the CMPINC specifications in the description assume that the seismograms have been rotated in t
3. networks and sources with seismic stations within this study area These data were actually contained in multiple directories e g TA network data from 2010 separate from ANSS network data from 2009 but were all part of the same project in FuncLab A project directory contains all the raw data used by FuncLab as well as files and directories it creates when a user initiates a new project A new project is created within the FuncLab GUI by importing at least one data directory of the structure defined in section 3 The following shows the structure of the automatically generated project directory RFPROJECT top directory no naming restriction ERDAN data directory for the imported SAC files eer same as RF data directory structure ae 2006 319 11 14 13 event directory MEE radial receiver function Updated April 17 2011 5 TA JOSA 0 6 i eat transverse receiver function TA_JO8A_0 6 i r radial seismogram TA_JO8A_0 6 i t transverse seismogram TA_JO8A_0 6 1 z vertical seismogram TA_KO9A Des Event_ Logfile txt log file Project mat project file CCPDATA data directory for the CCP stacks CCPData mat data file contains rays and depth axes Bin_1_000360_040080 mat stack file Bin_BIN _ BAZ RAYP mat Bin_2_000360_040080 mat ata directo or the Stacks GCCPDDATA data d ry for the GCCP k GCCPData mat data file cont
4. te_pref_fieldnames m te preferences gui m te view record m map ufilifes Updated April 17 2011 11 azimuth m deg2km m deg2rad m gg2gc m km2deg m latlon_from m rad2deg m utilities colvector m ignoreNaN m makeColorMap m mmpolar m skm2srad m srad2skm m Updated April 17 2011 APPENDIX B WEBSITE REFERENCES Seismic Analysis Code SAC http www iris edu software sac manual html Standing Order for Data SOD http www seis sc edu sod Receiver Function Codes Charles Ammon Penn State http eqseis geosc psu edu cammon HTML RftnDocs thecodes01 html Generic Mapping Tools GMT http www soest hawaii edu gmt Earthscope Automated Receiver Survey EARS http ears iris washington edu MATLAB Mapping Data e Coastlines O gshhs 2 1 1 http www ngdc noaa gov mgg shorelines data gshhs version2 1 1 gshhs _ e Topography O l arc minute DEM ETOPOI ice c 12 Ice Surface http www ngdc noaa gov mgg global relief ETOPO 1 data ice_surface ce ll registered binary etopol ice c 12 zip ETOPOI1 bed c i2 Bedrock Surface http www ngdc noaa gov mgg global relief ETOPO 1 data bedrock cell_r egistered binary etopo1 bed c i2 zip 2 arc minute DEM ETOPO2v2c_i2 MSB http www ngdc noaa gov mgg global relief ETOPO2 ETOPO2v2 2006 ETOPO2v2c raw_binary ETOPO2v2c_i2_MSB zip 30 arc second 1 km grid DEM GLOBE DEM http www ngdc noaa gov mgg topo DATATILES elev all10g zip
5. the seismograms are below NPTS 4401 number of points in seismogram B 1 000000e 01 beginning time of seismogram E 1 000000e 02 end time of seismogram IFTYPE TIME SERIES FILE defines the type of file LEVEN TRUE defines the sampling of the seismogram as even this is a MUST DELTA 2 500000e 02 Updated April 17 2011 14 sample rate of the seismogram IDEP UNKNOWN type of dependent variable not necessary for our purposes although we assume it is a velocity seismogram DEPMIN 1 740033e 02 minimum amplitude in seismogram DEPMAX 1 473583e 02 maximum amplitude in seismogram DEPMEN 8 144172e 01 mean amplitude in seismogram OMARKER 721 03 number of points in the time series TIMARKER 0 P arrival time and marker of predicted P wave this needs to be set as your zero time for the seismograms KZDATE AUG 14 227 2008 origin date of earthquake KZTIME 00 18 41 200 origin time of earthquake IZTYPE BEGIN TIME defines the reference time for this file needs to be set to BEGIN TIME KSTNM GOSA station code CMPAZ 0 000000e 00 component of motion azimuth needs to be 0 for vertical BAZ 180 for radial and radial RFs and BAZ 90 for transverse and transverse RFs CMPINC 0 000000e 00 component of motion inclination needs to be 0 for vertical and 90 for radial or transverse including RFs STLA 4 529040e 01 station latitude STLO 1 189595e 02
6. 0 6 1 z vertical seismogram file NET STA GAUSSIAN i 7 TA_KO9A Event_ Each file begins with the station name code contains the Gaussian parameter used to compute the receiver function and ends with i egr I have included files for both the radial and transverse receiver functions for completeness I also include the radial transverse and vertical seismograms to exploit some of the plotting features within the FuncLab toolbox All five of these files are required for a single station and single event Since FuncLab was originally designed for iterative time domain receiver functions the SAC files include the fit of the predicted waveform in the USER9 header the Gaussian parameter in the USERO header and the P wave ray parameter in sec rad in the USER1 header An additional setting for pre edited data has been added to the USERS If USERS is set to 1 the receiver function is marked as turned on and is used in the rest of the analyses If USERS is set to 0 the receiver function is marked as turned off and is discarded from analyses If USER8 is not set the default status is set to 1 and turned on 4 Project Directory Structure and Description A FuncLab project defines an entire dataset to be analyzed It can contain multiple data directories as defined in section 3 For example when developing this code my work was focused on the Pacific Northwest US I had collected data from a variety of
7. FuncLab MATLAB receiver function analysis toolbox Version 1 5 Author Kevin C Eagar User Manual Contents 1 ABOUT FUNCLAB 2 DOWNLOAD AND SETUP 3 RECEIVER FUNCTION DATA DIRECTORY STRUCTURE 4 PROJECT DIRECTORY STRUCTURE AND DESCRIPTION 5 MODEL BUILDING AND SETUP VELOCITY AND TOMOGRAPHY MODELS 6 ADD ON PACKAGES APPENDIX A LIST OF M FILES APPENDIX B APPENDIX C DESCRIPTION OF SAC FILES Updated April 17 2011 1 About FuncLab FuncLab comprises a set of tools built within the MATLAB environment The tools were developed on the Mac OS X platform beginning in 2006 with MATLAB 7 1 0 21 R14 student version Most of the developed tools were created to be compatible with this version but were not tested to be backwards compatible with earlier versions of MATLAB Figure dimensions may also vary from platform to platform and reflect the most recent development on Red Hat Linux 5 3 running MATLAB 7 9 0 R2009b Recent testing was also conducted on Mac OS X 10 6 7 running MATLAB 7 10 0 R2010a without problems There are some tools that are used within the toolkit that were not originally developed with FuncLab but are borrowed from free open source forums on the web The names and brief description of these scripts are as follows 1 ignoreNaN m is used to handle NaN values within matrices 2 makeColorMap m is used to adjust color maps in figures 3 mmpolar m creates a polar plot of ray parameter vs backazimuth 2 Download a
8. LES setup funclab m funclab m addons ccp gccp hk ccp_1D_raytracing m ccp_assign m ccp_binmap m ccp_binstack m ccp_bootstrap m ccp_Callback m ccp_corrections m ccp_ex_pp m ccp_ex_stacks m ccp fieldnames m ccp_migration m ccp_readamps m ccp_ record fields m ccp_ setup grid m ccp_stacking m cep m init_ccp m gcecp_1D_raytracing m gccp_assign m gcecp_binmap m gccp_binstack m gecp bootstrap m gcecp Callback m gccp_corrections m gccp_ex_pp m gccp ex _volume m gccp_fieldnames m gccp_migration m gccp_readamps m gccp_ record fields m gccp setup grid m gecp stacking m gccp m init gecp m hk allstack m Updated April 17 2011 10 hk Callback m hk ex grids m hk ex solutions m hk record fields m hk singlestack m hk view baz image m hk view hkgrid m hk view moveout image m hk view stacked records m hk m init hk m custom flab errordlg kce m movegui kce m guestdlg kce m uigetdir kce m uigetfile kce m fl add data gui m fl add new data m fl datainfo m fl datastats gui m fl default prefs m fl edit logfile m fl init logfile m fl log_gui m fl pref fieldnames m fl_preferences_gui m fl readseismograms m fl record_fields m fl traceedit gui m fl view baz image m fl view baz m fl view data coverage m fl view event map m fl view moveout image m fl_view_moveout m fl_view_record_section m fl_view_record m fl_view_stacked_records m fl_view_station_map m te_default_prefs m
9. ains rays and depth axes Bin 1 000360_040080 mat stack file Bin 2 000360 040080 mat HKDATA data directory for the H stacks TA JOSA 000360 040080 mat stack file NET STA BAZ RAYP mat TA KO9A 000360 040080 mat RFPROJECT this is a generic name given for the purposes of illustration is the top directory name which the user specifies at the onset of a new project The RAWDATA directory contains all the data directories that a user imports into the project Notice that these are of the same structure as described in the previous section The Logfile txt is a text file that is used to store a log of all the processes run within FuncLab on a specific project It contains a description of the process parameters used and time stamps This is generated automatically and can be useful when retrieving a record of the different runs for each process The Project mat file isa MATLAB formatted data file that contains all the MATLAB variables used to reference the raw seismic data and metadata within a project It is essentially the key database of the project There are also variables contained in Project mat that are used to communicate with the different GUIs of FuncLab and keep them talking to one another Other directories will be added under RFPROJECT once certain add on packages are initiated with a project These new directories are CCPDATA GCCPDATA and HKDATA Each of these contains MAT files storing
10. don t need to worry about this The Callback is followed by ccp_Callback which is important Keep this the same except the word ccp Callback This refers to a function or m file by the same name So replace ccp with whatever your add on name is Updated April 17 2011 8 This brings us to the third reguired component a callback function that transfers the FuncLab GUI handles to your add on GUI This is essential to connecting the core package with the add on This callback function must be named add on Callback m and must be in the add on directory As before replace add on with its proper name In my case of course it is called ccp_Callback m It must contain 4 lines of code as follows function ccp_Callback Ccbo eventdata handles h guidataCgcbf Project getCh project_t string ccpCh Replace ccp Callback with the name of your callback function And replace ccp h with your m file that begins the add on GUI The input h is the FuncLab GUI handles that MUST pass to the Add on GUI for things to work properly The final step is to create this m file that calls the Add on GUI It can have any structure The only difference is that when you want to use handles that are associated with the main FuncLab GUI you must refer to them in the input structure array This is clearer if you look at the examples provided with this manual Updated April 17 2011 APPENDIX A LIST OF M FI
11. he direction of the earthquake along the plane of the surface Rotations into true radial and transverse along the back projected ray path will have a different inclination Updated April 17 2011 16
12. ies to the search paths in MATLAB In addition this script checks for the Mapping and Signal Processing Toolboxes on the machine If these are installed certain functions will be available for use However if they are not installed some functions may not be available If the user has administrative rights on the machine running FuncLab they may choose to insert the full pathname of the setup funclab script to the startup m file located under the MATLAB application directory See MATLAB documentation for startup m for specifics see http Awww mathworks com help techdoc ref startup html This will then enable setup funclab to run automatically at the start of MATLAB FuncLab is now ready to be used on your machine 3 Receiver Function Data Directory Structure In order for this toolbox to function in a more general sense with publicly available data certain choices were necessary as to the data formats and directory structures expected by FuncLab The current version is only capable of importing seismic data that is in the SAC format http www iris edu software sac manual html It can read and handle SAC files that are either little endian or big endian byte order automatically It also requires a specific directory structure for the seismic data import and the creation of a new FuncLab project next section This directory structure originated from the output of publicly available data download using the Standing Order for Data SOD p
13. location to put it relative to the FuncLab directories In funclab m the path of the funclab command is searched for That path should be the same path that the flab directory is housed This is the directory that contains all of the core FuncLab code Place the add on directory in the addons subdirectory For example my cep directory contains all the codes for this add on It is placed under addons which is the same directory level as the flab directory and funclab m Make sure all the code that you use for the add on is in this directory It will not recognize any directories UNDER the main one though such as addons gt ccp gt working As a point of organization I prefer to name m files with the prefix of the add on directory e g ccp_assign m The next component is an m file under this add on directory called init_ add on m Replace add on with the name of the add on In my case it would be called init_ccp m This file need only contain 1 line that looks like this uimenuCMAddons Label Common Conversion Point Stacking Tag ccp m Enable off Callback ccp_Callback The string after Label is the name that you want it to read under the Add ons toolbar in the main FuncLab GUI Tag should just be some name that is unique I use the add on name as a prefix and the letter m which stands for main Enable should ALWAYS be off Don t worry it does get turned on eventually but you
14. ls in text files under the funclab1 5 VELMODELS directory and with the extension vel Otherwise FuncLab will not be able to find these models Tomography Models Certain analysis packages such as CCP and GCCP stacking can utilize seismic tomography models for timing corrections with receiver function time to depth conversions or migrations This version of FuncLab is distributed with a P wave tomography model of the Pacific Northwest published in West et al 2009 and used for CCP stacking analysis in Eagar et al 2010 It is placed under the funclab1 5 TOMOMODELSY directory in the MAT file NWUS_P09b_1 2 mat This file stores 6 variables used to define the model Depths Lons Lats ModelP ModelS and TomoType The first 5 are 3x3 matrices where the first second and third dimensions define x y and z longitudes latitudes and depth of the 3D volume The ModelP and ModelS variables define the P and S wave perturbations or velocities respectively at each point in the volume TomoType either defines the model as a perturbation model Dziewonski A M and D L Anderson 1981 Preliminary reference Earth model Phys Earth Planet Int 25 297 356 3 Kennett B L N and E R Engdahl 1991 Traveltimes for global earthquake location and phase identification Geophys J Int 105 429 465 3 Kennett B L N Engdahl E R and R Buland 1995 Constraints on seismic velocities in the Earth from travel times Geophys J In
15. nd Setup This section will introduce the step by step instructions for downloading and setting up the M files in the FuncLab package for your MATLAB session For the purposes of this manual UNIX and MATLAB command line inputs are typed in courier font file names and MATLAB variables are in italics and directory names are bolded FuncLab is distributed in a tar ball and can be accessed at http geophysics asu edu funclab Download and untar funclab tar in the directory in which you would like to place the MATLAB M files by typing tar xvf funclabl 5 tar The directory funclab1 5 will contain the files needed to run all the functions within the FuncLab toolbox Appendix A contains a list of all the M files Note that data for mapping functions requires the Mapping Toolbox may be downloaded from outside data sources Links to these data and other relevant websites are provided in Appendix B of this manual and on the FuncLab website These data include DEM or topography such as ETOPOI ETOPO2v2c and GLOBE DEM as well as GSHHS coastline data I recommend placing these under funclab1 5 map_data In order to use the FuncLab functions the user will need to add the paths to the files in the MATLAB session To perform this task the user must change to the funclabl1 5 directory and then run the setup funclab script Updated April 17 2011 3 cd funclabl 5 setup funclab The setup funclab script automatically adds all the director
16. rogram http www seis sc edu sod The choice of pre processing methods to obtain receiver functions is independent of FuncLab and is left up to the user however keep in mind that I developed this code using an iterative deconvolution receiver function code written by Charles Ammon at Penn State University The link to download this code is also posted on the FuncLab website Also posted are some generic C shell scripts that I originally used to run the preprocessing of data in this directory structure and output filenames appropriately We will assume that all of these steps have been completed Note that we are currently working with the IRIS DMS http www iris edu dms products to create a data product for direct import into FuncLab It will piggyback onto the EARS project http ears iris washington edu and perform all of the preprocessing steps on the front end The data directories should be structured in the follow manner RFDATA top directory to contain data can be named anything Event_2006 319 11 14 13 event directory Event YYYY JJJ HH MM SS TA_JO8A_0 6 i eqr radial receiver function file NET STA GAUSSIAN i egr TA_JO8A_0 6 i eqt transverse receiver function file NET STA GAUSSIAN i egt Updated April 17 2011 4 TA JOSA 0 6 ir radial seismogram file NET STA GAUSSIAN i r TA_JO8A_0 6 i t transverse seismogram file NET STA GAUSSIAN i TA_JO8A_
17. t 122 108 124 West J D M J Fouch J B Roth and L T Elkins Tanton 2009 Vertical mantle flow associated with a lithospheric drip beneath the Great Basin Nature Geoscience 2 439 444 Eagar K C M J Fouch and D E James 2010 Receiver function imaging of upper mantle complexity beneath the Pacific Northwest United States Earth Planet Sci Lett 297 141 153 Updated April 17 2011 7 or a velocity model to handle differencing the volume from the 1D velocity model used in the ray tracing As with velocity models other tomography models can be built to be used in FuncLab These new models should be place under the funclab1 5 TOMOMODELS and have the extension mat 6 Add on Packages These are special code packages that are optional with FuncLab running as the backdrop For instance I want to perform common conversion point stacking with some receiver function dataset to look at mantle discontinuities I have created a CCP Add on package that performs tasks that help me accomplish my goal and look at the data in a way that makes sense Although this package is integrated with FuncLab it is also separate from the FuncLab main code This means that the core package does NOT have to be altered to change things associated with the CCP package It means that anyone can write their own separate add on for whatever process they want to perform There is a specific directory structure needed for an add on and specific
18. variables created in MATLAB specific for the types of analyses performed For example the CCPDATA directory contains CCPData mat which stores variables that define the CCP grid and ray tracing information for each receiver function used in the stacks It also contains a separate MAT file for each CCP bin e g Bin_1_000360_040080 mat that stores variables defining the CCP stack for that bin This is similar for GCCPDATA Updated April 17 2011 6 The HKDATA directory contains a separate MAT file for each H x stack e g TA_F10A_000360_040080 mat The first and second set of numbers in the bin and H K stack files refers to the backazimuthal range and ray parameter range in the stacking respectively 5 Model Building and Setup Velocity Models Velocity models are an essential part of any seismic analysis FuncLab is at this point only designed to handle 1D Earth models in a very simple way This version of the package contains three commonly used 1D models PREM IASP917 and AK135 These are contained under the funclab1 5 VELMODELSYS directory within the text files PREM vel IASP91 vel and AK135 vel respectively Each contains three columns where column 1 is depth column 2 is Vp and column 3 is Vs Each row represents a new depth shell beginning at the depth defined in column 1 Other models can easily be built to use in FuncLab In order for FuncLab to recognize these however it is necessary to place the new velocity mode
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