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wphase:documentation [2015/01/27 17:49]
wphase [Getting the code]
wphase:documentation [2022/01/10 07:39] (current)
wphase [Extracting data from a gzipped tar archive]
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   - gcc and gfortran   - gcc and gfortran
   - python2.7 (or later)   - python2.7 (or later)
-  - You have to install numpy, matplotlib and basemap ​to run some python scripts which make figures.+  - You have to install numpy, matplotlib, cartopy ​and netCDF4 ​to run some python scripts which make figures.
   - rdseed   - rdseed
-  - GMT4 
  
-To install these dependencies on MacOs, ​you can refer to [[wphase:​macos|this page]].+To install these dependencies on MacOs, [[wphase:​macos|you can refer to this page]].
 ==== Building the code ==== ==== Building the code ====
  
 To install the code, we must first setup a few environment variables. If you use csh or tcsh: To install the code, we must first setup a few environment variables. If you use csh or tcsh:
 <​code>​ <​code>​
-setenv GMT_BIN ​     /​path/​to/​gmt/​bin 
 setenv RDSEED ​      /​path/​to/​rdseed/​executable setenv RDSEED ​      /​path/​to/​rdseed/​executable
 setenv GF_PATH ​     /​path/​to/​greens/​functions/​database setenv GF_PATH ​     /​path/​to/​greens/​functions/​database
-setenv WPHASE_HOME ​ /​path/​to/​wphase/package+setenv WPHASE_HOME ​ /​path/​to/​wphase
 </​code>​ </​code>​
 If you use bash: If you use bash:
 <​code>​ <​code>​
-export GMT_BIN=/​path/​to/​gmt/​bin 
 export RDSEED=/​path/​to/​rdseed/​executable export RDSEED=/​path/​to/​rdseed/​executable
 export GF_PATH=/​path/​to/​greens/​functions/​database export GF_PATH=/​path/​to/​greens/​functions/​database
Line 91: Line 88:
  
 ----- -----
 +
 +==== Extracting data from a gzipped tar archive ====
 +As SEED volumes are no longer supported, waveforms and instrument response can also be extracted from a gzipped tar archive (hereafter referred to as "​tgz"​) including both SAC and SAC_PZ (poles and zeros) files. ​
 +Instead of using the "​extract.csh"​ script to extract data from SEED, we can then extract data from a tgz archive using: ​
 +<​code>​${WPHASE_HOME}/​bin/​tgz2DATA_org.py path_to_tgz_archive.tgz</​code> ​
 +where "​path_to_tgz_archive.tgz"​ is the path to the tgz archive including SAC and SAC_PZ files. This script will extract SAC and SAC_PZ files a the directory named "​DATA_org"​.
 +
 +Two tgz archive formats are supported: WILBER (default) and NIED. 
 +
 +Using the WILBER format, the tgz archive should include SAC files named with a "​.SAC"​ or "​.sac"​ extension and SAC_PZ file names starting with "​SAC_PZ"​. If data is ordered using the [[https://​ds.iris.edu/​wilber3|IRIS Wilber 3 system]], this format can be obtained directly by selecting "​Output format: SAC binary"​ (little or big-endian) ​ and "​Bundle As: gzipped tar archive"​ in the final Request Data page (see below). ​
 +
 +{{:​wilber3_screenshot.png?​300|{{:​wphase:​wilber3_screenshot.png?​300|}}
 +
 +Once the tgz archive is prepared, extraction from a WILBER formatted archive is done by running:
 +<​code>​${WPHASE_HOME}/​bin/​tgz2DATA_org.py path_to_tgz_archive.tgz wilber</​code> ​
 +As this is the default format, the "​wilber"​ option can be removed from the command line.
 +
 +Using the NIED tgz archive format, SAC_PZ files should end with "​.zp"​ and SAC file names can have any format (but should not end with "​.zp"​). Extraction from a NIED archive can be done using 
 +<​code>​${WPHASE_HOME}/​bin/​tgz2DATA_org.py path_to_tgz_archive.tgz nied</​code> ​
 +
 +---
  
 ==== Calculating Synthetics, deconvolution and filtering ==== ==== Calculating Synthetics, deconvolution and filtering ====
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 $WPHASE_HOME/​bin/​wpinversion -ifil o_wpinv.th1.3 -ofil o_wpinv.th0.9 -th 0.9  $WPHASE_HOME/​bin/​wpinversion -ifil o_wpinv.th1.3 -ofil o_wpinv.th0.9 -th 0.9 
 </​code>​ </​code>​
-  - Finally, it is possible to remove the channels showing a large rms ratios (observed/​predicted and predicted/​observed) using the option –nr (e.g. –nr 2.0): <​code>​+  - Finally, it is possible to remove the channels showing a large rms amplitude ​ratios (observed/​predicted and predicted/​observed) using the option –nr (e.g. –nr 2.0): <​code>​
 $WPHASE_HOME/​bin/​wpinversion -ifil o_wpinv.th0.9 -ofil o_wpinv.th1.3 -nr 2.0 $WPHASE_HOME/​bin/​wpinversion -ifil o_wpinv.th0.9 -ofil o_wpinv.th1.3 -nr 2.0
 </​code>​ </​code>​
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 ----- -----
 ==== RUNA scripts ==== ==== RUNA scripts ====
-Data extraction, ​screening and inversion ​described above can be performed by running one of the RUNA3*csh scripts (usually in bin). These scripts ​perform data extraction/screening and calculate a moment tensor solution after median data screening and after rejecting ​ traces associated with large misfit using the threshold 5.0 3.0 0.9 (i.e. -th, see 2. in section ​4):+Data screening and inversion can all be done at once using the RUNA3_lite.csh script: 
 +<​code>​ 
 +${WPHASE_HOME}/​bin/​RUNA3_lite.csh 
 +</​code>​ 
 +This script can be used after data extraction in "​DATA_org"​ using either "​tgz2DATA_org.py"​ or "​extract.csh"​ to extract data from a tgz archive or a SEED volume, respectively (see above). Once the "​DATA_org"​ directory is populated, the "​RUNA3_lite.csh"​ script will perform data screening and calculate a moment tensor solution after median data screening and after rejecting ​ traces associated with large misfit using the threshold 5.0 3.0 0.9 (i.e. -th, see 2. in the "​Inversion" ​section ​above)
 + 
 +If data is extracted directly from SEED volume(s), data extraction/​screening and inversion can be done directly by running:
 <​code>​ <​code>​
 ${WPHASE_HOME}/​bin/​RUNA3.csh ${WPHASE_HOME}/​bin/​RUNA3.csh
 </​code> ​ </​code> ​
-will perform median and rms misfit screening for Z, N, E, 1 and 2  channels,+To do the inversion on "Z" components only (i.e.not using the horizontals)use:
 <​code>​ <​code>​
 ${WPHASE_HOME}/​bin/​RUNA3_only_Z.csh ​ ${WPHASE_HOME}/​bin/​RUNA3_only_Z.csh ​
 </​code>​ </​code>​
-will perform median and rms misfit screening for Z channels only. 
  
-These two scripts don’t perform the “ratio screening” (i.e. 3. above). To run the same routines with an additional screening based on the ratio (observed/​predicted and predicted/​observed),​ the following ​scripts ​can be used:+These two scripts don’t perform the “ratio screening” (i.e. 3. in the "​Inversion"​ section ​above). To run the same routines with an additional screening based on the rms amplitude ​ratio (observed/​predicted and predicted/​observed),​ the following ​script ​can be used:
 <​code>​ <​code>​
 ${WPHASE_HOME}/​bin/​RUNA3r.csh ​ ${WPHASE_HOME}/​bin/​RUNA3r.csh ​
 </​code>​ </​code>​
 will perform median, rms misfit and rms ratio for channels Z, N, E, 1, 2 channels, will perform median, rms misfit and rms ratio for channels Z, N, E, 1, 2 channels,
 +Warning: RUNAr.csh is not yet fully tested.
  
-Remark: RUNAr.csh is not yet fully tested. 
- 
- 
-Several optional parameters can be used when running RUNA3*csh scripts. These parameters will apply to the wpinversion program. They are described when running wpinversion -h.  
-e.g.:  RUNA3.csh -wz 1.0 -wn 0.3 -we 0.5  will give a weights of 1.0, 0.3 and 0.5 for Z, N, E components respectively. 
- 
-To perform data screening and inversion only, using previously extracted SAC data, it is possible to use:  
-<​code>​ 
-${WPHASE_HOME}/​bin/​RUNA3_lite.csh 
-</​code>​ 
-that is designed for Z, N ,Z ,1, 2 channels 
  
 ----- -----
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 ==== Plot routines ==== ==== Plot routines ====
  
-All the plotting scripts are coded using python and the module pylab which have to be installed before using them. The module ​basemap ​is also needed for plotting maps but it is optional (even if we recommend to install it).+All the plotting scripts are coded using python and the module pylab which have to be installed before using them. The module ​cartopy ​is also needed for plotting maps but it is optional (even if we recommend to install it).
  
 There are 3 script which can be used to plot the W phase inversion results: There are 3 script which can be used to plot the W phase inversion results:
  
    * The first script is <​code>​${WPHASE_HOME}/​bin/​make_grids.py</​code>​ which be used to display grid-searches results. Use <​code>​${WPHASE_HOME}/​bin/​make_grids.py -h</​code>​ to have more details on available options and arguments. The 2 other scripts plot observed and synthetic seismograms after W phase inversion. ​    * The first script is <​code>​${WPHASE_HOME}/​bin/​make_grids.py</​code>​ which be used to display grid-searches results. Use <​code>​${WPHASE_HOME}/​bin/​make_grids.py -h</​code>​ to have more details on available options and arguments. The 2 other scripts plot observed and synthetic seismograms after W phase inversion. ​
-   * In order to plot complete seismograms individually and place station on a map: <​code>​${WPHASE_HOME}/​bin/​traces_global.py</​code>​ which draw complete seismograms and show station location on a map (if basemap ​is available). Please use <​code>​${WPHASE_HOME}/​bin/​traces_global.py -h</​code>​ for more details on available options.+   * In order to plot complete seismograms individually and place station on a map: <​code>​${WPHASE_HOME}/​bin/​traces.py</​code>​ which draw complete seismograms and show station location on a map (if cartopy ​is available). Please use <​code>​${WPHASE_HOME}/​bin/​traces.py -h</​code>​ for more details on available options.
    * To plot concatenated waveforms:<​code>​${WPHASE_HOME}/​bin/​make_cwp.py</​code>​ For more details on available options and arguments see <​code>​${WPHASE_HOME}/​bin/​make_cwp.py -h</​code>​ to see the options.    * To plot concatenated waveforms:<​code>​${WPHASE_HOME}/​bin/​make_cwp.py</​code>​ For more details on available options and arguments see <​code>​${WPHASE_HOME}/​bin/​make_cwp.py -h</​code>​ to see the options.
 +
 +-------
 +
 +===== Using ETOPO01 Global Relief Model =====
 +
 +ETOPO01 is a 1 arc-minute global relief model of the Earth'​s surface
 +provided by Amante et al. (2009):
 +<​http://​www.ngdc.noaa.gov/​mgg/​global/​global.html>​
 +
 +If Cartopy is installed, you can optionally draw ETOPO01 topography and
 +bathymetry. To do so, the path to the ETOPO01 netCDF file must be
 +assigned to the environment variable $ETOPOFILE which can be
 +done in your .tcshrc fil (or .bachrc, .cshrc, etc.). The make_grids.py
 +script have been tested only for grid-registered netCDF file of the
 +ETOPO1 bedrock file available at:
 +<​http://​www.ngdc.noaa.gov/​mgg/​global/​relief/​ETOPO1/​data/​bedrock/​grid_registered/​netcdf/​ETOPO1_Bed_g_gmt4.grd.gz>​
 +
  
 ------- -------
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 ${WPHASE_HOME}/​bin/​make_grids.py –p -b  ${WPHASE_HOME}/​bin/​make_grids.py –p -b 
 </​code>​ </​code>​
-to create the file grid_search_xy.pdf containing Fig. 1 which corresponds to the above example. The option –b is optional: it allows to use the basemap ​module in order to plot coastlines and topography.+to create the file grid_search_xy.pdf containing Fig. 1 which corresponds to the above example. The option –b is optional: it allows to use the cartopy ​module in order to plot coastlines and topography.
wphase/documentation.1422377346.txt.gz · Last modified: 2015/01/27 17:49 by wphase