Software package to calculate strain tensor parameters
StrainTool allows the estimation of Strain Tensor parameters, on the earth's crust, given a list of data point, aka points on the earth along with their tectonic velocities.
StrainTool has three basic components:
- A python package, named
pystrain - The main executable, named
StrainTensor.py - A list of shell scripts to plot results from
StrainTensor.py
A first application of the software with EUREF data was presented in EGU2019 (Anastasiou et al. 2019).
pystrain is a package written in python, defining a variety of functions, classes, etc to enable the computation of strain tensors.
When installing this package, all of its modules will be available to the user. It is the core part of the project and should be installed before the main program (StrainTensor.py) can be used.
The package is found under StrainTool/pystrain
This is the main program, i.e the program that the user will run to produce strain tensor results. It is heavily dependant on the pystrain package (so any change there will affect StrainTensor.py's behaviour
This program does not need installation; it is just a pyrhon script. The user may only need to change priviledges to make it executable
StrainTensor.py is located at StrainTool/bin
By 'Plot Tools', we mean an array of shell (Bash) scripts that can be used to plot StrainTensor.py results. These scripts actualy use GMT to perform the plotting. The scripts are efficient, ready-to-use.
It is by no means mandatory to use these scripts to plot the results; users can use their own tools and/or scripts to do so. Actually, this is a totaly independent part of the Project and can be skipped alltogether.
These scripts, are found under StrainTool/plot
To install the Project, you will need:
- python; the installation has been tested under Versions 2.7 and 3.6 and both work fine.
- NumPy; NumPy is the fundamental package for scientific computing with Python.
- SciPy; SciPy is a Python-based ecosystem of open-source software for mathematics, science, and engineering. Actually, we are only using the SciPy.linalg and SciPy.spatial modules.
Both NumPy and SciPy have extended installation guides for most, if not all, operating systems.
To use the Plot Tools bundle, you must have GMT (> 5.0.0) installed, along with a variety of UNIX-based tools. If you are on a UNIX/Linux operating system, most or all of them are pre-installed.
To install the Project, you actualy only need to install the pystrain package. What this means, is that python will see that the package modules are build and extracted to a suitable folder on your local system (something like /usr/lib/python2.7/site-packages/ on a UNIX-like system). After this step, you will be able to make use of the modules in the package, both for running StrainTool.py and for any new program you may wish to code. StrainTensor.py and Plot Tools are programs, so you do not to "install" them.
To install pystrain, do the following:
-
go to the directory the package is located, i.e.
StrainTool/pystrain -
the package comes with a
setup.pyscript, so you only need to run it (as root/administrator):$> python setup.py install
That's it! The package modules should now be in place and you should be able to use the main script, StrainTensor.py
The following scenarios have been tested to validate the installation procedure
| OS | Python 2.7 | Python 3.6 | Python 3.10 | GMT 5.2 | GMT 5.4 | GMT 6.3 |
|---|---|---|---|---|---|---|
| Fedora | ✅ | ✅ | ||||
| Manjaro | ✅ | ✅ | ✅ | ✅ | ||
| Ubuntu | ✅ | ✅ | ✅ | ✅ | ✅ | ✅ |
| Windows 10 | ✅ | ✅ | ✅ | ✅ | ✅ |
To validate that the installation has succeeded, you can run various "test case" scenarios. In the data/ folder, you will find a subfolder named valdata/ that contains the script runtests.py. This script will execute all the validation tests and compare the results with the reference outputs.
We use four input files (midas00[1-4].vel), which are generated from the original station velocity file (midas.IGS14.txt) (Blewitt, 2018), within different grid boxes.
Reference results are produced using different parameters. The first 16 characters of the filename represent the various parameters as follows:
## Parameters codes
# 1: [0: reference results 1:product]
# 2: File [1:midas001 2:midas002, 3:midas003, 4:midas004]
# 3: step grid [0:0.5/0.5, 1:1/1, 2:0.25/0.25, 3:0.1/0.1 4:2/2]
# 4: -c [0:no 1:yes]
# 5: -b barycenter [0:False 1:set]
# 6-7: Wt [<=99]
# 8-9: dmin [< 100 km]
# 10-12: dmax [001 - 999]
# 13-14: dstep [01--99]
# 15: -g generate statistics [0:False, 1:true]
# 16: --multicore [0:False, 1:True]
Velocity files and reference results are stored at refdata.7z.
All the files must be extracted at valdata/ subfolder and then runtests.py pyhton script can executed with the follow command:
$> python runtests.py -p <path to StrainTool root path>
The script will run all the available tests and compare the results with the reference files to validate the installation.
StrainTensor.py computes strain tensor parameters on a selcted grid. The program comes with an extended help message, that can be displayed via the -h or --help switch (aka
$> ./StrainTensor.py [...] --help
will show the help message on screen). Users can control StrainTensor.py's behaviour via a variety of available switches.
To use the program, the only mandatory switch is the -i or --input-file, which specifies the input file to be used. All other options will automaticaly assume default values (see Options for a detailed list). Basic usage is described below:
usage: StrainTensor.py [-h] -i INPUT_FILE [--x-grid-step X_GRID_STEP]
[--y-grid-step Y_GRID_STEP] [-m METHOD] [-r REGION]
[-c] [-b] [--max-beta-angle MAX_BETA_ANGLE]
[-t WEIGHTING_FUNCTION] [--Wt Wt] [--dmin D_MIN]
[--dmax D_MAX] [--dstep D_STEP] [--d-param D_PARAMETER]
The whole list of available options, is:
optional arguments:
-h, --help show this help message and exit
-i INPUT_FILE, --input-file INPUT_FILE
The input file. This must be an ascii file containing the columns: 'station-name longtitude latitude Ve Vn SigmaVe SigmaVn Sne time-span'. Longtitude and latitude must be given in decimal degrees; velocities (in east and north components) in mm/yr. Columns should be seperated by whitespaces. Note that at this point the last two columns (aka Sne and time-span) are not used, so they could have random values.
--x-grid-step X_GRID_STEP
The x-axis grid step size in degrees. This option is only relevant if the program computes more than one strain tensors. Default is 0.5(deg).
--y-grid-step Y_GRID_STEP
The y-axis grid step size in degrees. This option is only relevant if the program computes more than one strain tensors. Default is 0.5(deg)
-m METHOD, --method METHOD
Choose a method for strain estimation. If 'shen' is passed in, the estimation will follow the algorithm described in Shen et al, 2015, using a weighted least squares approach. If 'veis' is passed in, then the region is going to be split into delaneuy triangles and a strain estimated in each barycenter. Default is 'shen'.
-r REGION, --region REGION
Specify a region; any station (in the input file) falling outside will be omitted. The region should be given as a rectangle, specifying min/max values in longtitude and latitude (using decimal degrees). E.g. "[...] --region=21.0/23.5/36.0/38.5 [...]"
-c, --cut-excess-stations
This option is only considered if the '-r' option is set. If this option is enabled, then any station (from the input file) outside the region limit (passed in via the '-r' option) is not considered in the strain estimation.
-b, --barycenter Only estimate one strain tensor, at the region's barycentre.
--max-beta-angle MAX_BETA_ANGLE
Only relevant for '--method=shen'. Before estimating a tensor, the angles between consecutive points are computed. If the max angle is larger than max_beta_angle (in degrees), then the point is omitted (aka no tensor is computed). This option is used to exclude points from the computation that only have limited geometric coverage (e.g. the edges of the grid). Default is 180 deg.
-t WEIGHTING_FUNCTION, --weighting-function WEIGHTING_FUNCTION
Only relevant for '--method=shen'. Choose between a 'gaussian' or a 'quadratic' spatial weighting function. Default is 'gaussian'.
--Wt Wt Only relevant for '--method=shen' and if 'd-param' is not passed in. Let W=Σ_i*G_i, the total reweighting coefficients of the data, and let Wt be the threshold of W. For a given Wt, the smoothing constant D is determined by Wd=Wt . It should be noted that W is a function of the interpolation coordinate, therefore for the same Wt assigned, D varies spatially based on the in situ data strength; that is, the denser the local data array is, the smaller is D, and vice versa. Default is Wt=24.
--dmin D_MIN Only relevant for '--method=shen' and if 'd-param' is not passed in. This is the lower limit for searching for an optimal d-param value. Unit is km. Default is dmin=1km.
--dmax D_MAX Only relevant for '--method=shen' and if 'd-param' is not passed in. This is the upper limit for searching for an optimal d-param value. Unit is km. Default is dmax=500km.
--dstep D_STEP Only relevant for '--method=shen' and if 'd-param' is not passed in. This is the step size for searching for an optimal d-param value. Unit is km. Default is dstep=2km.
--d-param D_PARAMETER
Only relevant for '--method=shen'. This is the 'D' parameter for computing the spatial weights. If this option is used, then the parameters: dmin, dmax, dstep and Wt are not used.
-g, --generate-statistics
Only relevant when '--mehod=shen' and '--barycenter' is not set. This option will create an output file, named 'strain_stats.dat', where estimation info and statistics will be written. (default: False)
--verbose Run in verbose mode (show debugging messages) (default: False)
--multicore Run in multithreading mode (default: False)
-v Display version and exit. (default: False)
For example, the command:
$> ./StrainTensor.py -i ../data/<input-file> -r 18.75/30.25/32.75/42.25 --x-grid-step=0.5 --y-grid-step=0.5 --dmin=1 --dmax=500 --dstep=1 --Wt=24 -c -g
meant that we are estimating strain tensor parameters for the region within min/max longtitude: 18.75/30.25 degrees and min/max latitude: 32.75/42.25 degrees. We are seperating the region into cells of size 0.5 degrees and estimating one strain tensor in each cell centre (aka the first cell centre is
To perform the computations, StrainTensor.py needs an input file, that holds input data. Usually, this implies a list of GPS/GNSS stations with their ellipsoidal coordinates (aka longtitude and latitude) and their respective tectonic velocities (usually estimated using position time-series) along with the corresponding standard deviation values. The format of these files, should follow the convention:
station-name longtitude latitude Ve Vn SigmaVe SigmaVn Sne time-span
string deg. deg. mm/yr mm/yr mm/yr mm/yr / dec. years
Station coordinates are provided in longtitude/latitude pairs in decimal degrees. Velocities and velocity standard deviations are provided in mm per years (mm/yr). Sne is the correlation coefficient between East and North velocity components and time-span is the total time span of the station timeseries in decimal degrees. Note that at this point the last two columns (aka Sne and time-span) are not used, so they could have random values.
There are no strict formating rules on how the individual elements should be printed (i.e. how many fields, decimal places, etc). The only condition is that fields are seperated by whitespace(s). To see an example of a valid input file, you can check data/valdata/valdata.7z/midas00[1-4].vel.
Note that when using the Shen method (aka --method='shen'), standard deviation values for north and east velocities (SigmaVe and SigmaVn) cannot be zero (see #65).
Results of StrainTensor.py are recorded in the following three files:
- strain_info.dat : This file includes strain tensor parameters, principal axis, rotational rates, dilatation etc.
The columns of the file are structured as below:
Latitude Longtitude vx+dvx vy+dvy w+dw exx+dexx exy+dexy eyy+deyy emax+demax emin+demin shr+dshr azi+dazi dilat+ddilat sec.inv.+dsec.inv. deg deg mm/yr mm/yr deg/Myr nstrain/yr nstrain/yr nstrain/yr nstrain/yr nstrain/yr nstrain/yr deg. nstrain/yr nstrain/yr
- station_info.dat : Stations' data used for the calculation of strain tensor are written at htis file. Format is:
Code Longtitude Latitude Ve Vn dVe dVn string deg deg mm/yr
- strain_stats.dat : Output file for statistics:
--HEADER--
Parameters and arguments used for estimation of strain tensors.
--statistics--
Longtitude Latitude # stations D (optimal) CutOff dis. Sigma
deg. deg. # Km # /
Plotting scripts are placed under plot/ directory. They are:
gmtstrainplot.sh,gmtstatsplot.sh, andplotall.sh
All of the scripts need the file named default-param to be in the same folder.default-param file options
pth2inptf=../data/ # set default folder for input files (strain_info.dat, strain_stats.dat, station_info.dat) west, east, south, north, projscale, frame, sclength: set region parameters PAPER_SIZE="30cx30c" : set custom paper size (width x height) vscmagn=20 : magnitude of horizontal arrow scale VSC=0.05 : Horizontal velocity scale strscmagn=100 : set magnitude of principal axes scale STRSC=0.01 : set principal axis plot scale ROTSC=.7 : set rotational rates plot scale ROT_wedge_mag=1 : set magnitude of rotational 1-wedge.
gmtstrainplot.sh options:
Basic Plots & Background :
-r | --region : region to plot (default Greece)
usage: -r west east south north projscale frame
Plot station and velocities:
-psta [:=stations] plot only stations from input file
-deltr [:= delaunay triangles] plot delaunay triangles
-vhor (station_file)[:= horizontal velocities]
-vsc [:=velocity scale] change valocity scale default 0.05
Plot strain tensor parameters:
-str (strain file)[:= strains] Plot strain rates
-rot (strain file)[:= rots] Plot rotational rates
-gtot(strain file)[:=shear strain] plot total shear strain rate contours
-gtotaxes (strain file) dextral and sinistral max shear strain rates
-dil (strainfile)[:= dilatation] Plot dilatation and principal axes
-secinv (strain file) [:=2nd invariand] Plot second invariand
-strsc [:=strain scale]
-rotsc [:=rotational scales]
*for -gtot | -dil | -secinv use +grd to plot gridded data
ex:-gtot+grd
Other options:
-o | --output : name of output files
-l | --labels : plot labels
-mt | --map_title "text": title map default none, use quotes
-jpg : convert eps file to jpg
-h | --help : help menu
For example, to plot the principal axis fo strain rates for the example case above you can use the following command:
$> ./gmtstrainplot.sh -jpg -str strain_info.dat -psta -l
gmtstatsplot.sh options:
Basic Plots & Background :
-r | --region : region to plot (default Greece)
usage: -r west east south north projscale frame
Plot Stations and triangles:
-psta [:=stations] plot only stations from input file
-deltr [:= delaunay triangles] plot delaunay triangles
Plot Statistics:
-stats (input file) set input file
--stats-stations : plot used stations
--stats-doptimal : plot optimal distance (D)
--stats-sigma : plot sigma
Other options:
-o | --output : name of output files
-l | --labels : plot labels
-leg : plot legends
-mt | --map_title : title map default none, use quotes
-jpg : convert eps file to jpg
-h | --help : help menu
For example, to plot the principal axis fo strain rates for the example case above you can use the following command:
$> ./gmtstatsplot.sh -jpg -stats strain_stats.dat --stats-stations -leg -o output_stats-stations
plotall.sh options:
- no switch produce default output names -p | --prefix : add prefix work id to output file -s | --suffix : add suffix work id to output file -h | --help: help panel
$> ./plotall.sh -p test -s test2
v1.0-rc2.0 The calculation of second invariant was corrected due to a mistake in the previous version (v1.0-rc1.0))
- Calculating strains at the North or South Pole using UTM (Universal Transverse Mercator) is problematic because UTM zones converge at the poles, making it impractical for coordinate transformations from ellipsoid to projected coordinates in those regions. Working on that bug!!
- Create an issue and describe your idea
- Fork it
- Create your feature branch (
git checkout -b my-new-idea) - Commit your changes (
git commit -am 'Add some feature') - Publish the branch (
git push origin my-new-idea) - Create a new Pull Request
- Profit! ✅
The work is licensed under MIT-license
Prof. Dimitrios G. Anastasiou
Assistant Professor NTUA | Dionysos Satellite Observatory - NTUA | danastasiou@mail.ntua.gr
Dr. Xanthos Papanikolaou
Dr. Rural & Surveying Engineer | Dionysos Satellite Observatory - NTUA | xanthos@mail.ntua.gr
Dr. Athanassios Ganas
Research Director | Institute of Geodynamics | National Observatory of Athens | aganas@gein.noa.gr
Prof. Demitris Paradissis
Professor NTUA | Dionysos Satellite Observatory - NTUA | dempar@central.ntua.gr
The history of releases can be viewed at ChangeLog
This project has received funding from:
EPOS IP - EPOS Implementation Phase funded from the European Union’s Horizon 2020 research and innovation programme under grant agreement N° 676564
Geo-INQUIRE funded by the European Commission under project number 101058518 within the HORIZON-INFRA-2021-SERV-01 call
Disclaimer: the content of this website reflects only the author’s view and the Commission is not responsible for any use that may be made of the information it contains.
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Anastasiou D., Ganas A., Legrand J., Bruyninx C., Papanikolaou X., Tsironi V. and Kapetanidis V. (2019). Tectonic strain distribution over Europe from EPN data. EGU General Assembly 2019, Geophysical Research Abstracts, Vol. 21, EGU2019-17744-1 Abstract
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Shen, Z.-K., M. Wang, Y. Zeng, and F. Wang, (2015), Strain determination using spatially discrete geodetic data, Bull. Seismol. Soc. Am., 105(4), 2117-2127, doi: 10.1785/0120140247
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Veis, G., Billiris, H., Nakos, B., and Paradissis, D. (1992), Tectonic strain in greece from geodetic measurements, C.R.Acad.Sci.Athens, 67:129--166
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Python Software Foundation. Python Language Reference, versions 2.x/3.x. Available at http://www.python.org
For validation data:
- Blewitt, G., W. C. Hammond, and C. Kreemer (2018), Harnessing the GPS data explosion for interdisciplinary science, Eos, 99, https://doi.org/10.1029/2018EO104623.
