Merge pull request #51 from DSOlab/dev-danast

Dev danast

Author: DemAnasta

.github/CHANGELOG.md

@@ -1,5 +1,40 @@
 # Change Log
 
+## [v1.0-rc4.0](https://github.com/DSOlab/StrainTool/tree/v1.0-rc4.0)(2018-12-14)
+
+[Full Changelog](https://github.com/DSOlab/StrainTool/compare/v1.0-rc3.0...v1.0-rc4.0)
+
+**Implemented enhancements:**
+
+- rotational units [\#33](https://github.com/DSOlab/StrainTool/issues/33)
+- Issue33 [\#45](https://github.com/DSOlab/StrainTool/pull/45) ([demanasta](https://github.com/demanasta))
+
+**Fixed bugs:**
+
+- gmtplots: scale of gridded data not plotted correctly [\#47](https://github.com/DSOlab/StrainTool/issues/47)
+- -r / --region switch fails if not set [\#44](https://github.com/DSOlab/StrainTool/issues/44)
+- Issue47  [\#50](https://github.com/DSOlab/StrainTool/pull/50) ([demanasta](https://github.com/demanasta))
+- Issue33 [\#48](https://github.com/DSOlab/StrainTool/pull/48) ([demanasta](https://github.com/demanasta))
+- Dev [\#46](https://github.com/DSOlab/StrainTool/pull/46) ([demanasta](https://github.com/demanasta))
+
+**Merged pull requests:**
+
+- sync issue33 wth dev-danast [\#43](https://github.com/DSOlab/StrainTool/pull/43) ([demanasta](https://github.com/demanasta))
+- sync dev-danast with master [\#41](https://github.com/DSOlab/StrainTool/pull/41) ([demanasta](https://github.com/demanasta))
+
+## [v1.0-rc3.0](https://github.com/DSOlab/StrainTool/tree/v1.0-rc3.0) (2018-11-30)
+[Full Changelog](https://github.com/DSOlab/StrainTool/compare/v1.0-rc2.0...v1.0-rc3.0)
+
+**Implemented enhancements:**
+
+- Issue38 [\#39](https://github.com/DSOlab/StrainTool/pull/39) ([demanasta](https://github.com/demanasta))
+
+**Fixed bugs:**
+
+- gmtstrainplot python verion error [\#38](https://github.com/DSOlab/StrainTool/issues/38)
+- gmtplots: gtotalaxes [\#37](https://github.com/DSOlab/StrainTool/issues/37)
+- Issue38 [\#39](https://github.com/DSOlab/StrainTool/pull/39) ([demanasta](https://github.com/demanasta))
+
 ## [v1.0-rc2.0](https://github.com/DSOlab/StrainTool/tree/v1.0-rc2.0) (2018-11-27)
 [Full Changelog](https://github.com/DSOlab/StrainTool/compare/v1.0-rc1.0...v1.0-rc2.0)
 

README.md

@@ -39,9 +39,9 @@ This program does not need installation; it is just a pyrhon script. The user ma
 
 ## Plot Tools
 
-By 'Plot Tools', we mean an array of shell ([Bash](https://www.gnu.org/software/bash/)) scripts that can be used to plot `StrainTensor.py` results. These scripts actualy use [GMT](http://gmt.soest.hawaii.edu/) to perform the plotting. The scripts are an efficient, ready-to-use
+By 'Plot Tools', we mean an array of shell ([Bash](https://www.gnu.org/software/bash/)) scripts that can be used to plot `StrainTensor.py` results. These scripts actualy use [GMT](http://gmt.soest.hawaii.edu/) 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. Actualy, this is a totaly independent part of the Project and can be skipped alltogether.
+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`
 
@@ -53,11 +53,11 @@ To install the Project, you will need:
 
 *   [python](https://www.python.org/downloads/); the installation has been tested under Versions 2.7 and 3.6 and both work fine.
 *   [NumPy](http://www.numpy.org/); NumPy is the fundamental package for scientific computing with Python.
-*   [SciPy](https://www.scipy.org/); SciPy is a Python-based ecosystem of open-source software for mathematics, science, and engineering. Actualy, we are only using the [SciPy.linalg](https://docs.scipy.org/doc/scipy/reference/linalg.html) and [SciPy.spatial](https://docs.scipy.org/doc/scipy/reference/spatial.html) modules.
+*   [SciPy](https://www.scipy.org/); SciPy is a Python-based ecosystem of open-source software for mathematics, science, and engineering. Actually, we are only using the [SciPy.linalg](https://docs.scipy.org/doc/scipy/reference/linalg.html) and [SciPy.spatial](https://docs.scipy.org/doc/scipy/reference/spatial.html) modules.
 
 Both `NumPy` and `SciPy` have extended installation guides for most, if not all, operating systems.
 
-To use the [Plot Tools](#plot_tools_pck) bundle, you must have [GMT](http://gmt.soest.hawaii.edu/) (> 5.0.0) installed, allong 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 use the [Plot Tools](#plot_tools_pck) bundle, you must have [GMT](http://gmt.soest.hawaii.edu/) (> 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.
 
 ## Installation Procedure
 
@@ -74,14 +74,14 @@ That's it! The package modules should now be in place and you should be able to
 
 ### Installation tests
 
-The following scenarios have been tested to validatethe installation procedure
+The following scenarios have been tested to validate the installation procedure
 
 |    OS      |Python 2.7 | Python 3.6 | GMT 5.2 | GMT 5.4
 |:----------:|:------------------:|:------------------:|:------------------:|:------------------:|
 | Fedora     | :white_check_mark: |                    | :white_check_mark: |                   |
 | Manjaro    |                    | :white_check_mark: | :white_check_mark: |                   |
 | Ubuntu     | :white_check_mark: | :white_check_mark: | :white_check_mark: | :white_check_mark: |
-| Windows 10 | :white_check_mark: |                    |                    |                    |
+| Windows 10 | :white_check_mark: | :white_check_mark: | :white_check_mark: | :white_check_mark: |
 
 
 ## Example
@@ -104,7 +104,7 @@ Under `data/` you will find the "reference" output files for checking, named `st
 
     $> ./StrainTensor.py [...] --help
 
-will show the help message on screen). Users can controll `StrainTensor.py`'s behaviour via a variety of available switches.
+will show the help message on screen). Users can control `StrainTensor.py`'s behaviour via a variety of available switches.
 
 ## Basic Usage
 
@@ -148,13 +148,13 @@ The whole list of available options, is:
 
 For example, the command we used on the [Example](#straintensor_prg_example) section:
 
-    $> ./StrainTensor.py -i ../data/CNRS_midas.vel -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
+    $> ./StrainTensor.py -i ../data/CNRS_midas.vel -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 $lon = lon_{min} + lon_{step}/2 = 18.75 + 0.5/2=19.0deg.$ and $lat = lat_{min} + lat_{step}/2 = 32.75 + 0.5/2 = 33.0deg.$, then next one will be at lon=19.5, lat=33.5, etc...). To estimate each strain tensor, the program will search for a "optimal" D coefficient within the range [1, 500) km with a step of 1km. This "optimal" D will be found when the condition $W = \sum_{n=1}^{\#sta*2} Z(i)*L(i) \geq W_t$ is met. The stations that will be used for the calculations are only those that fall within the specified longtitude/latitude range. For more information, see [Background and Algorithms](#bck_and_algorithms) section.
 
 ## Input Files
 
-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) allong with the corresponding standard deviation values. The format of these files, should follow the convention:
+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:
 
 <pre id="block-samp" <samp="">        station-name  longtitude   latitude   Ve     Vn    SigmaVe  SigmaVn  Sne  time-span 
          string           deg.        deg.   mm/yr  mm/yr   mm/yr    mm/yr    /   dec. years</pre>
@@ -171,7 +171,7 @@ Results of `StrainTensor.py` are recorded in the following three files:
     The columns of the file are structured as below:
 
 <pre id="block-samp" <samp="">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. invariant 
-   deg       deg         mm/yr           mm/yr          marcsec/yr       nstrain/yr      nstrain/yr      nstrain/yr      nstrain/yr      nstrain/yr      nstrain/yr         deg.         nstrain/yr      nstrain/yr   
+   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   
 	        </pre>
 
 *   **station_info.dat :** Stations' data used for the calculation of strain tensor are written at htis file. Format is:
@@ -181,7 +181,7 @@ Code    Longtitude Latitude  Ve   Vn   dVe  dVn
 string      deg       deg          mm/yr
 	      </pre>
 
-*   **StrainTensor.out :** Parameters used to modigy grid, calculate Strain tensors etc.
+*   **StrainTensor.out :** Parameters used to modify grid, calculate Strain tensors etc.
 
 # How to use Plot Tools
 
@@ -196,8 +196,17 @@ All of the scripts need the file named `default-param` to be in the same folder.
 <pre id="block-samp" <samp="">   
 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.
 </pre>
 
 **gmtstrainplot.sh options:**
@@ -229,7 +238,7 @@ Other options:
      -h | --help : help menu
 </pre>
 
-For exanple, to plot the principal axis fo strain rates for the example case above you can use the following command:
+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
 
@@ -259,7 +268,7 @@ Other options:
      -h | --help : help menu
 </pre>
 
-For exanple, to plot the principal axis fo strain rates for the example case above you can use the following command:
+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
 

StrainWebTool/config.py

@@ -20,7 +20,7 @@
 ############################################## ploting
 from scipy.spatial import Delaunay
 
-Version = 'StrainTensor.py Version: 1.0-rc3.0'
+Version = 'StrainTensor.py Version: 1.0-rc4.0'
 
 def cut_rectangle(xmin, xmax, ymin, ymax, sta_lst, sta_list_to_degrees=False):
     new_sta_lst = []
@@ -229,7 +229,7 @@ class myFormatter(
 ##+ If cutting out-of-limits stations option is set, or method is veis, then 
 ##+ only keep the stations that fall within it.
 ##  The region coordinates (min/max pairs) should be given in decimal degrees.
-if args.region:
+if 'region' in args:
     try:
         lonmin, lonmax, latmin, latmax = [ float(i) for i in args.region.split('/') ]
         if args.cut_outoflim_sta or args.method == 'veis':
@@ -245,7 +245,7 @@ class myFormatter(
         print('[ERROR] Failed to parse region argument \"{:}\"'.format(args.region), file=sys.stderr)
 
 ##  Filter out stations that are never going to be used. This is an opt!
-if args.region and not args.method == 'veis' and not args.cut_outoflim_sta:
+if 'region' in args and not args.method == 'veis' and not args.cut_outoflim_sta:
     vprint('[DEBUG] Filtering stations based on their distance from region barycentre.')
     Napr = len(sta_list_ell)
     mean_lon, mean_lat = radians(lonmin+(lonmax-lonmin)/2e0), radians(latmin+(latmax-latmin)/2e0)
@@ -288,7 +288,7 @@ class myFormatter(
 fout = open('strain_info.dat', 'w')
 vprint('[DEBUG] Strain info written in file: {}'.format('strain_info.dat'))
 print('{:^9s} {:^9s} {:^15s} {:^15s} {:^15s} {:^15s} {:^15s} {:^15s} {:^15s} {:^15s} {:^15s} {:^15s} {:^15s} {:^15s}'.format('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. invariant'), file=fout)
-print('{:^9s} {:^9s} {:^15s} {:^15s} {:^15s} {:^15s} {:^15s} {:^15s} {:^15s} {:^15s} {:^15s} {:^15s} {:^15s} {:^15s}'.format('deg', 'deg', 'mm/yr', 'mm/yr', 'marcsec/yr', 'nstrain/yr', 'nstrain/yr', 'nstrain/yr', 'nstrain/yr', 'nstrain/yr', 'nstrain/yr', 'deg.', 'nstrain/yr', 'nstrain/yr'), file=fout)
+print('{:^9s} {:^9s} {:^15s} {:^15s} {:^15s} {:^15s} {:^15s} {:^15s} {:^15s} {:^15s} {:^15s} {:^15s} {:^15s} {:^15s}'.format('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'), file=fout)
 
 ##  Compute only one Strain Tensor, at the region's barycenter; then exit.
 if args.one_tensor:
@@ -305,7 +305,7 @@ class myFormatter(
     ##+ is not passed in, the grid.generate_grid will transform lon/lat pairs 
     ##+ to degrees and produce a grid from extracting min/max crds from the
     ##+ station list.
-    if args.region:
+    if 'region' in args:
         grd = pystrain.grid.Grid(lonmin, lonmax, args.x_grid_step, latmin, latmax, args.y_grid_step)
     else:
         grd = pystrain.grid.generate_grid(sta_list_ell, args.x_grid_step, args.y_grid_step, True)

StrainWebTool/run.py

@@ -12,7 +12,7 @@ outfile=output.ps
 # #colormaps
 # landcpt=land_man.cpt
 # bathcpt=bath_man.cpt
-
+PAPER_SIZE="30cx30c" # width x height
 
 # //////////////////////////////////////////////////////////////////////////////
 # Set default REGION 
@@ -28,16 +28,17 @@ sclength=100
 
 logo_pos="BL/.1c/.1c"
 
-# scale position parameters for velocities
-vsclon=22.34
-vsclat=37.68
+# scale parameters for velocities
+# vsclon=22.34 #delete
+# vsclat=37.68 #delete
 vscmagn=20
 VSC=0.05
 
 strscmagn=100
 STRSC=.0080
-ROTSC=.7
-strsclon=20.4
-strsclat=36.3
+ROTSC=.65
+ROT_wedge_mag=1 #(deg/My)
+# strsclon=20.4 #delete
+# strsclat=36.3 #delete
 
 legendc="-Jx1i -R0/8/0/8 -Dx20.5c/12.6c+w5c/4.6c+jBL"