Intarsis GMTSAR Automatic Processing workflow

These programs generate an automatic processing flow to monitor zones by applying GMTSAR SBAS routine. It is intended to work in Linux systems with a working GMTSAR and GMT installation. It is recommended to have also a recent version of gdal, if you have a old system use Anaconda to install updated versions.

Intarsis must be copied in a folder declared in the $PATH varible. It is written in bash. You can run the different steps inside a folder with the following required input files:

• dem.grd: Dem for the region of interest. You can download it from https://topex.ucsd.edu/gmtsar/demgen/ . Altitudes must be in WGS84 heights (ellipsoidal heights). GMTSAR can use higher resolution DEMs but it must be in EPSG:4326 and netCDF format and nodata value set to NaN.
• SAFE_filelist: File with full path to the SLC files to use. The zips must be uncompressed in *SAFE folders. The SLC can be outside of processing folder.
• pins.ll: File with the coordinates of the region of intererest.
• batch_tops.config: file with interferogram parameters. You can modify it with the appropiate parameters for your site.

Optional files

• Intarsis.config: (recommended) configuration file with some parameters for the automatization of the processing.
• orbits.list: list of orbit files. If it is not provided the gmtsar will download from ASF. But if the machine does not have Internet access or ASF server is down it can be provided and Intarsis will use.

Description of the routines:

Intarsis_00_run_all

Routine to run all steps from 01 to 06. It will log everything in intarsis.runall.log. The parameters must be configured via intarsis.config.

Intarsis_01_file_preparation

This program check all the input files, creates the folder structure and cut the SLC acording to the pins.ll file.

Intarsis_02_allign

This program does the corregistration for each Interferometric Swath. You must input the desired swath (F1,F2 or F3) as parameter and the master master date (or create a master_image file).

Intarsis_03_intf

This program generates the interferograms, using "parallel" (check that is installed in your system).

Intarsis_04a_merge

(Optional step) Merge two or three swaths together before the unwrap. Currently under develop.

Intarsis_04b_mask

(Optional step) Creation of a coherence mask to speedup unwrap step.

Intarsis_05_unwrap

Unwrapping of the phase.

Intarsis_06_sbas

Generates intf.tab and scene.tab files for SBAS and runs the code

Intarsis_09_reset_*

Some routines to remove some steps if you want to redo it.

Other useful tools

Sentinel1_orbit_downloader (https://github.com/krasny2k5/sentinel1_orbit_downloader)

This program will download the orbit archive from ESA Sentinel-1 QC server and store in the same folder as the program. It is recommended to speed up the processing since it is faster than download the fil from asf server, however the orbit archive is quite big (about 15Gb as Dec 2019).

update_gmt5sar

Small script to download, compile and install GMTSAR. It is recommended for updates, not for initial installation because the first compilation can have unmet depedencies problems.

ortho2ellip

Program that adds the EGM08 heights to a orthonormal DEM and convert into GMTSAR netcdf format and projection. It needs the EGM08 altitudes file and the input DEM must be readable by gdal and with declared srs.

Other recommendations:

• Some distros do not compile GMT with BLAS/LAPACK support, so some steps can be slower. It is recommended to use when possible, so you might consider to recompile GMT to add these features.