GMTSAR

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INSTRUCTIONS FOR INSTALLING AND RUNNING GMTSAR

Copyright (c) 2009-2017 David T. Sandwell - dsandwell@ucsd.edu Xiaohua Xu - xix016@ucsd.edu Rob Mellors - rmellors@geology.sdsu.edu Xiaopeng Tong - xitong@ucsd.edu Meng Wei - mwei@ucsd.edu Paul Wessel - pwessel@hawaii.edu

This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; version 3 of the LICENSE.TXT

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

Significant Modifications: February 13, 2010 March 11, 2010 March 25, 2010 June 8, 2010 September 27, 2010 April 4, 2013 Converted to use GMT API and redone the entire install procedure. Linking with GMT means GMTSAR will use the FFTs recognized by GMT: Accelerate Framework on OS X, FFTW, KISS FFT, or Brenner Fortran-translated FFT. GMT selects the fastest FFT given the dimensions and the availability of libraries.

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1. Obtain GMT from SOEST and install [see "Obtaining GMT" on gmt.soest.hawaii.edu]. Make sure all the required libraries (e.g., netcdf, GDAL, PCRE) have been installed before you start the GMT build/install procedure.

2. Go to the GMTSAR WIKI and follow the instructions. http://gmt.soest.hawaii.edu/projects/gmt5sar/wiki

3. Download orbit files for ERS and ENVISAT. No need for ALOS orbit data because it is built in raw file. The file is > 1G and contains all the available orbit for ERS and ENVISAT. It takes a while to download but you only need to download it once. Put it anywhere you like; let's refer to this dir as

   http://topex.ucsd.edu/gmtsar/downloads

4. Obtain GMTSAR subversion. Go to the GMTSAR WIKI and follow the instructions. http://gmt.soest.hawaii.edu/projects/gmt5sar/wiki

   autoconf

   (When we install you can specify a system directory such as /usr/local, assuming you have permission).

5. Configure GMTSAR: Run the configure script. To see all options, run

   ./configure --help

   Most users will simply run

   ./configure --with-orbits-dir= --prefix=

   where was defined in step (3) and is where you want to place all the executables. For example, you might run

   ./configure --with-orbits-dir=/usr/local/orbits

   If you are a developer you may also want to add --enable-debug so you can run the programs in a visual debugger. Note: If you ever decide to move the orbits directory then you must also reconfigure GMTSAR.

6. To build all executables, type make Assuming that went well, you can install executables, scripts, and shared data by running make install or sudo make install if you are writing to a system directory that requires admin privileges. After this step you can remove your staging directory/tar-files if you like.

7. test the commands: gmt, esarp, xcorr, conv, gmtsar.csh, etc. If using C-shell you may have to type rehash first. If this does not work then make sure the is in your system $PATH or $path.

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RUN

1. GET DATA. There is an example data set at our website:

http://topex.ucsd.edu/gmtsar/downloads/

Uncompress the file and then unpack with tar.

2. ORGANIZE the DISK. The standard GMTSAR run has the following directories.

raw SLC topo intf

raw - contains the original data.

SLC - contains the single look complex images derived from the raw data.

topo - contains a digital elevation model for the area in geographic and ultimately radar coordinates.

intf - contains subdirectories with the possible interferograms (only 1 for this example).

In raw, original data have special name format. If you got data that have different name system, you need to change the name according to the following:

For ALOS we just need the IMG- and LED-files. Here is an example. -rw-r--r-- 1 sandwell 14 382547520 Aug 28 15:29 IMG-HH-ALPSRP227730640-H1.0__A -rw-r--r-- 1 sandwell 14 12506972 Aug 28 15:28 LED-ALPSRP227730640-H1.0__A -rw-r--r-- 1 sandwell 14 12506972 Aug 28 15:28 LED-ALPSRP207600640-H1.0__A -rw-r--r-- 1 sandwell 14 747383820 Aug 28 15:28 IMG-HH-ALPSRP207600640-H1.0__A

Make sure the images are all from the same orbit direction, same track, and same frame. The filename ALPSRP207600640-H1.0__A can be decomposed as:

__A - ascending 0640 - frame number 20760 - orbit number To check that the data are from the same track, the difference between orbit numbers should be divisible by 671. In this case there are 7, 46-day cycles between the acquisitions.

For ENVISAT we just need .baq file. Here is an example. ENV1_2_084_2943_42222.baq ENV1_2_084_2943_42723.baq

The filename means: ENVISAT _ 2 _ track number _ frame number _ orbit number

For ERS we just need .dat and .ldr file. Here is an example. e2_127_2907_23027.ldr e2_127_2907_23027.dat e2_127_2907_23528.ldr e2_127_2907_23528.dat

The filename means: ERS2_track number_frame number_orbit number. .dat - raw data file .ldr - leader file

3. MAKE DEM

Go to the following web site and construct a file dem.grd that encloses the SAR frame. http://topex.ucsd.edu/gmtsar/demgen

Place the file dem.grd in the /topo directory.

4. DO EVERYTHING

For ALOS: p2p_ALOS.csh IMG-HH-ALPSRP207600640-H1.0__A IMG-HH-ALPSRP227730640-H1.0__A configure.txt

The file configure.txt should be edited to set a number of parameters including the starting point for t he InSAR processing.

For ENVISAT: p2p_ENVI.csh ENV1_2_084_2943_42222 ENV1_2_084_2943_42723 dem.grd

For ERS: p2p_ERS.csh e2_127_2907_23027 e2_127_2907_23528 dem.grd

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RUN - STEP-BY-STEP INSTRUCTIONS

Taking ALOS for example but applicable to ERS and ENVISAT.

1. PREPROCESS the raw data

   cd raw ls IMG* >> data.in

Edit the data.in file and place the master in the first line. Also one can set the -radius and -near_range on the first line to have this frame match other frames along the same track. When this command is done you will have PRM and raw files for every scene in the list data.in, all in the same format and geometry. Execute the command.

pre_proc_batch.csh ALOS data.in

2. ALIGN the SLC images. Link the raw data into the SLC directory. cd SLC cp ../raw/.PRM . ln -s ../raw/.raw . ln -s ../raw/LED* .

Align the images

align.csh ALOS IMG-HH-ALPSRP207600640-H1.0__A IMG-HH-ALPSRP227730640-H1.0__A 

This will keep your computer busy for a while. The first image is called the master and the second is a slave. One can align a slave to the master and then use that slave as a surrogate master. This is useful for alignment of a large stack of data having a large spread in the baseline versus time plot. When this is done you will have 2 output files for each scene, a PRM-file and a Single Look Complex (SLC-file). The PRM-files are ascii text files containing the parameters needed for InSAR processing.

master IMG-HH-ALPSRP207600640-H1.0__A.PRM IMG-HH-ALPSRP207600640-H1.0__A.SLC

slave IMG-HH-ALPSRP227730640-H1.0__A.PRM IMG-HH-ALPSRP227730640-H1.0__A.SLC

(Look inside the script align.csh to see what it does.)

3. MAKE the topo_ra.grd

   cd topo cp ../SLC/IMG-HH-ALPSRP207600640-H1.0__A.PRM master.PRM ln -s ../raw/LED-ALPSRP207600640-H1.0__A .

Next you will need a file dem.grd. Thus can be created at: http://topex.ucsd.edu/gmtsar/demgen

Once you have the dem.grd in lon/lat coordinates you can convert it to radar coordinates using the following command.

dem2topo_ra.csh master.PRM dem.grd

This creates a file called topo_ra.grd. The script also creates postscript images of the dem.ps and topo_ra.ps that can be viewed. The script also creates a file trans.dat that has the complete mapping from lon,lat,topo to range,azimuth. This same file will be used later for geocoding, (i.e., converting the range, azimuth grids back into lon, lat space).

4. INTERFEROGRAM

cd intf mkdir 20760_22773

Note these are the orbit numbers of the reference and repeat images. One could also use dates for the directory name.

cd 20760_22773 ln -s ../../raw/LED-ALPSRP207600640-H1.0__A . ln -s ../../raw/LED-ALPSRP227730640-H1.0__A . cp ../../SLC/IMG-HH-ALPSRP207600640-H1.0__A.PRM . cp ../../SLC/IMG-HH-ALPSRP227730640-H1.0__A.PRM . ln -s ../../SLC/IMG-HH-ALPSRP207600640-H1.0__A.SLC . ln -s ../../SLC/IMG-HH-ALPSRP227730640-H1.0__A.SLC . ln -s ../../topo/topo_ra.grd .

All these files are needed to be linked or copied to make the interferogram. Of course this could all be done with a script. Now make the interferogram. While it is running look inside the script intf.csh to see the grdmath. Also, if you have any kind of error, delete everything and start over.

intf.csh IMG-HH-ALPSRP207600640-H1.0__A.PRM IMG-HH-ALPSRP227730640-H1.0__A.PRM -topo topo_ra.grd

The output will be three grd and postscript files.

display_amp.grd, display_amp.ps - amplitude of interferogram phase.grd, phase.ps - phase of interferogram corr.grd, corr.ps - correlation of interferogram

The phase measures the displacement of the repeat images relative to the reference images. The "reference and repeat" is a separate definition from the "master and slave" (refer to the document). Note that the phase is relative measurement so it's not important whether the pixel values are negative or positive. Phase increase means that the ground is moving away from the radar (range increasing); phase decrease means that the ground is moving toward the radar (range decreasing).

5. FILTER INTERFEROGRAM

   filter.csh IMG-HH-ALPSRP207600640-H1.0__A.PRM IMG-HH-ALPSRP227730640-H1.0__A.PRM gauss_alos_200m 2

The gaussian filter and decimation for the amplitude and phase images are the same. filter is the name of the filter. decimation control the size of the amplitude and phase images. It is either 1 or 2. Set the decimation to be 1 if you want higher resolution images. Set the decimation to be 2 if you want images with smaller file size.

The output will be masked and filtered phase as well as phase gradients (xphase.grd and yphase.grd).

6. UNWRAP PHASE

   cd intf/20760_22773 shaphu.csh .10

7. GEOCODE

   cd intf/20760_22773 ln -s ../../topo/trans.dat . geocode.csh .10

This command will make postscript and KML images of the phase, correlation, and display amplitude. The argument 0.15 is used to mask the phase when the coherence is less than 0.15. Use your GMT skills to improve on these maps. One can combine the phase (color) and amplitude (shading) in gmt grdimage or combine the phase (color) and gmt grdgradient dem.grd (shading) to make interesting plots.

8. SHIFT THE TOPOPHASE [OPTIONAL]

The topo_ra.grd may not be perfectly aligned with the master SLC. This can be corrected by shifting the topo_ra by 1 or 2 pixels, usually in the range direction.

cd SLC slc2amp.csh IMG-HH-ALPSRP207600640-H1.0__A.PRM amp_master.grd cd ../topo ln -s ../SLC/amp_master.grd . offset_topo amp_master.grd topo_ra.grd 0 0 5 topo_shift.grd

The last line of the output from this program shows the shift needed to maximize the cross correlation between the amplitude of the master image and the range gradient of the topo_ra.grd. The output file is the topography shifted by an integer number of pixels. Now go back to step 4) and use the topo_ra_shift.grd instead of the topo_ra.grd to remake the interferogram.