intro to shells, sac, and gmt rob porritt uc berkeley phd candidate rob@seismo.berkeley.edu

Intro to shells, SAC, and GMT

Rob PorrittUC Berkeley PhD candidaterob@seismo.berkeley.edu

OutlineShells

HistoryScripting

SACGetting SAC InteractiveWithin a script

GMTExample script

Working on a terminal

History of shells1977 by Stephen Bourne at AT&T Bell Labs – the

bourne shell (/bin/sh)

1978 team at Berkeley – the C-shell (/bin/csh)

Bourne shell updated to the bourne again shell (/bin/bash)

C-shell updated to the TCSH shell (/bin/tcsh)

Many more, but these are the most common

Using shellsAnytime you use a terminal your are explicitly

using a shell

ScriptsBut you can also put a bunch of commands into

a script to run repeatedly!

Making a scriptFirst line:

#!/bin/tcsh

Tells the default shell to use the interpreter located at /bin/tcsh

Write a series of commands and #defines comments

chmod +x filename

./filename

Useful commandsssh – login to a remote computer

set – make a variable which can be returned with $var

foreach (tcsh)

screen – run a process not connected to a terminal (ctrl + a + d to detach. screen –r to reattach)

Getting SAChttp://www.iris.edu/software/sac/

sac.request.htm

Using SACCommand line

based Seismic Analysis Code

Set of tools to process data. Frequency filtering, decimation, fft, correlation, integration, differentiation, etc…

Raw data (counts)

Ground Velocity (m/s)

Doing it automaticallyMake a script!

GMTPaint by numbers

Start with example scripts and edit for new purposes

Rest of the time we’ll spend making a script to make a map of Socorro

Original tutorial by Andy Goodliffe at the University of Alabama – editted by Rob

You can use this script for future plots – just copy, paste, edit

Where did the data come from?

Space Shuttle Radar Topography Mission (SRTM) data

1 Arc-second (~30 m) grids

Downloaded from the USGS Seamless server (http://seamless.usgs.gov/) and converted to a GMT format (NetCDF) gridRe-sampled (using grdfilter) to a 0.0005 degree grid

Also available from NASA (ftp://e0srp01u.ecs.nasa.gov)

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•A transmit antenna illuminates the terrain with a radar beam which is scattered by the surface. Both arrays receive the reflected signal

•The signal coming to one antenna may have traveled slightly further than that arriving at the other

•This translates into a phase difference

•By measuring the phase difference we can determine the angle from which the signal came

•When combined with travel time, we can determine the distance to that point

The Basic C-ShellOpen your favorite text editor on the UNIX

system and create a file named plot_socorro_topo.gmt

File names are arbitrary – Make them reasonable so you know what they do

If you’re a glutton for punishment like me you can use VIM by typing vi plot_socorro_topo.gmt

Or you can use xemacs by typing xemacs plot_socorro_topo.gmt &The & at the end puts the xemacs command in the

background so that you get your prompt back

Anatomy….Indicates that the script is a TC-Shell

Sets a variable for the area of the map

Sets a variable for the tick marks on the map – annotations every 0.2 minutes, tick marks every 10 minutes

Sets a variable for the map projection and scale – in this case the projection is Mercator and the scale is such that the x-axis of the map is 5.5 inches long

Draws the basemap psbasemap and the four variables

Return to the terminal and type chmod +x plot_socorro_topo.gmtThen run the command with ./plot_socorro_topo.gmtView the plot with a viewer such as ggv (ie ggv socorro.ps)

Sets the format of the map annotation

misc variable contains other information:-V be verbose, -P portrait mode, -X2i shift by 2 inches in x

Make a variable for the output plot name

The Map…Hopefully your map looks something like this (depending on settings in your .gmtdefaults file)

Edit your C-Shell so that

set boundaries = “-Ba0.2f10m”

Now reads

set boundaries = “-BSWnea0.2f10m”

This will make it so that only the southern and western axes are labeled

Note: to find other options in psbasemap, simply type man psbasemap – this will display the help pages

Add TopographyYou have each been given a two files – socorro.grd and socorro.cpt – these are the SRTM grid files and color palette file respectively

grdimage will draw a color image of the topography in socorro.grd using the color palette (-C) socorro.cpt

>> indicates postscript code is being appended to the file created by the previous command

-O tells the interpreter to overlay this information on a previous map Run the c-shell

-K tells the interpreter there is more commands to be appended

The Map….White is the highest topography, brown is the lowest.We can all agree that this color palette is ugly – lets take a moment to create a new one using grd2cpt

Type man grd2cpt to see how to do this…. Or simply type grd2cpt

Changing the Color Palette

In this case I have used the haxby color palette – experiment with other palettes

Add Illumination

grdgradient creates an illumination file with simulated illumination from the north (-A0), dimensionless gradient (-M) normalized to 1 (-Nt). The output illumination file is socorro.grad

grdimage has had the paramter –I added to it. This indicates that the resultant image will be illuminated with the file socorro.grad

The grd2cpt command has been commented out – this does not need to be run any more

The Map….There is now a lot more information in the map – you can start to see structures and river channels

By changing the –A option in grdgradient, try recreating the image with different illumination angles. Does one angle help us to visualize structures better than another?

Add Contours

grdcontour creates a layer in the postcript file that will display contours every 100 m (-C100)

The grdgrdient command has been commented out – this does not need to be run any more

Note that we are now using –O and –K. This indicates that this is neither the top of bottom layer in the postscript file

The Map….We now have an idea of the size of the mountains around us – we know from running the script last time that the minimum and maximum contours are 1300 m and 3200 m respectively

By changing the –C option in grdcontour, change the contour interval to 200 m. By using the –A option, add annotations every 1000 m

Add A Color Scale

psscale draws a color bar using the color palette socorro2.cpt

This is the location (x – 1.25 inches, y = -0.5 inches) and size (4 x 0.25 inches). h indicates that the bar is horizontal

The bar is labeled every 500 m and annotated with “meters”

The Map….The uninitiated reader now everything they need to know most of the map details.

Why have I not added a regular scale bar?

Add the Location of the Library

psxy plots points on maps using a number of different methods (see man psxy). Typically we would read these points from a file, but since we are only plotting one point, we will read it from the C-Shell . psxy can also be used to plot a regular graph

A star (-Sa) with a 0.4 inch diameter is drawn

The line thickness of the star is 1 point (1p) and the line is black (0)

The color fill is the star is white (255)

As input, psxy reads until it reaches END

This is the longitude and latitude of the library

The Map….Colors in GMT are specified in RGB format – thus 255/0/0 is red, 0/255/0 is green, etc. You can mix colors to create the color of your choice. By changing the –G option in psxy, change the color of the star (for example, -G255/0/0 would make the star red),

Add Some Text to the Mapptext plots text on maps Typically we would read text strings from a file, but since we are only plotting one text string we will read it from the C-Shell

The font size is 14 points

The text will be black

This is the longitude and latitude at which the text will be plotted

The text will be plotted horizontally (0 degrees)

Font number 1 (helvetica) will be used

The text will be centered on the point (CM)

The Map….The text is plotted on top of the star. By changing the text justification (currently CM) and/or the text position, move the text so that it is under the star. You might want to also change the text color….

Add an Inset to the MapWe are adding more layers after psscale, so we have added a -K

We are redefining the area of the map – the inset will include the contiguous states. It will be 2 inches across

This creates the basemap for the inset. The background is white (-G255), axis are drawn without label or ticks (-Bnesw), and the origin is offset horizontally by 0.2 inches (-X0.2) and vertically by 7.65 (-Y7.65) inches relative to the previous basemapA black star is plotted at Socorro

pscoast is used to plot a low-resolution (-Dl) coastline is plotted. It has a line thickness of 1 point and is black

The Map….

What can you do with this map now? The postscript format image can be read by a number of other packages – Adobe Illustrator being one example….

This map was the end point for last year’s tutorial. If there’s time and willingness I can also show some other tools to extract data from a grid and use psxy for an xy data plot.

The full script with lots of comments is available on the resource website.

Code to make the profile

Extract xyz file info from the topo grid

If the latitude is right, spit out the longitude and elevation to psxy

With profile