updating plots, readme, and fixing typos in example script

Fixing plots of I2 to be in a log scale in several places.
Bumping version to 1.1.1

Author: kmaterna

Strain_Tools/strain/models/strain_visr.py

@@ -211,5 +211,7 @@ def check_fortran_executable(path_to_executable):
     if os.path.isfile(path_to_executable):
         print("VISR executable found at %s " % path_to_executable);
     else:
-        raise FileNotFoundError("VISR executable not found on your system. Check config file for path.");
+        raise FileNotFoundError("\n  ERROR!  VISR executable not found on your system. Check config file for path.  "
+                                "\n  If you don't have it on your local system, the source can be downloaded from: "
+                                "\n  http://scec.ess.ucla.edu/~zshen/visr/visr.html");
     return;

Strain_Tools/strain/output_manager.py

@@ -86,6 +86,7 @@ def outputs_1d(xcentroid, ycentroid, polygon_vertices, rot, exx, exy, eyy, range
     [I2nd, max_shear, dilatation, azimuth] = strain_tensor_toolbox.compute_derived_quantities(exx, exy, eyy);
     [e1, e2, v00, v01, v10, v11] = strain_tensor_toolbox.compute_eigenvectors(exx, exy, eyy);
     [positive_eigs, negative_eigs] = get_list_eigenvectors(xcentroid, ycentroid, e1, e2, v00, v01, v10, v11);
+    I2nd = np.log10(np.abs(I2nd));  # for convenient plotting
 
     dilatation_polygon_outfile = outdir + "Dilatation_polygons.txt"
     second_inv_polygon_outfile = outdir + "I2nd_polygons.txt"

code.json

@@ -3,7 +3,7 @@
     "name": "Strain_2D",
     "organization": "U.S. Geological Survey",
     "description": "Strain rate modeling from GNSS velocity fields using multiple published strain rate techniques.",
-    "version": "1.1.0",
+    "version": "1.1.1",
     "status": "RELEASE_STATUS",
 
     "permissions": {
@@ -16,10 +16,10 @@
       ]
     },
 
-    "homepageURL": "https://usgs.github.io/Strain_2D/",
-    "downloadURL": "https://github.com/usgs/Strain_2D/archive/master.zip",
-    "disclaimerURL": "https://github.com/usgs/Strain_2D/blob/master/LICENSE.md",
-    "repositoryURL": "https://github.com/usgs/Strain_2D.git",
+    "homepageURL": "https://code.usgs.gov/kmaterna/Strain_2D",
+    "downloadURL": "https://code.usgs.gov/kmaterna/Strain_2Darchive/master.zip",
+    "disclaimerURL": "https://code.usgs.gov/kmaterna/Strain_2D/blob/master/LICENSE.md",
+    "repositoryURL": "https://code.usgs.gov/kmaterna/Strain_2D.git",
     "vcs": "git",
 
     "laborHours": 0,

example/Display_output/comparison_rows_example.sh

@@ -3,7 +3,7 @@
 
 range=$1
 projection="M2.0i"
-out_strain="output_rows.ps"
+out_strain="output_rows_plots.ps"
 gmt set MAP_FRAME_TYPE plain
 gmt set FORMAT_GEO_MAP D
 
@@ -14,9 +14,10 @@ infile3=$output_dir"visr/visr_strain.nc"
 infile4=$output_dir"loc_avg_grad/loc_avg_grad_strain.nc"
 
 # Delaunay Strain
-gmt makecpt -T-1/5/0.5 -Cbatlow.cpt > mycpt.cpt
+gmt makecpt -T-1/5/0.5 -Cbatlow > mycpt.cpt
 gmt grdedit $infile1=gd?HDF5:"$infile1"://I2 -R$range -T -G$"I2_delaunay.nc" 
 gmt grdedit I2_delaunay.nc -Ev
+gmt grdmath I2_delaunay.nc ABS LOG10 = I2_delaunay.nc
 gmt grdimage I2_delaunay.nc -R$range -J$projection -BWeSn -Bp1.0 -Cmycpt.cpt -X2 -Y10 -K > $out_strain
 gmt pscoast -R -J -Wthick,black -Df -Sgray -K -O >> $out_strain
 echo "-122.8 42.3 Delaunay" | gmt pstext -R -J -F+f18p,Helvetica-Bold -N -K -O >> $out_strain
@@ -26,6 +27,7 @@ gmt psvelo $output_dir"delaunay/negative_eigs.txt" -Se0.003/0.68/0 -A+b+n10+pthi
 # Loc_Avg_Grad Strain
 gmt grdedit $infile4=gd?HDF5:"$infile4"://I2 -R$range -T -G$"I2_loc_avg_grad.nc" 
 gmt grdedit I2_loc_avg_grad.nc -Ev
+gmt grdmath I2_loc_avg_grad.nc ABS LOG10 = I2_loc_avg_grad.nc
 gmt grdimage I2_loc_avg_grad.nc -R$range -J$projection -BweSn -Bp1.0 -Cmycpt.cpt -X6 -Y0 -K -O >> $out_strain
 gmt pscoast -R -J -Wthick,black -Df -Sgray -K -O >> $out_strain
 echo "-122.8 42.3 Loc avg grad" | gmt pstext -R -J -F+f18p,Helvetica-Bold -N -K -O >> $out_strain
@@ -35,6 +37,7 @@ gmt psvelo $output_dir"loc_avg_grad/negative_eigs.txt" -Se0.003/0.68/0 -A+b+n10+
 # Visr Strain
 gmt grdedit $infile3=gd?HDF5:"$infile3"://I2 -R$range -T -G$"I2_visr.nc" 
 gmt grdedit I2_visr.nc -Ev
+gmt grdmath I2_visr.nc ABS LOG10 = I2_visr.nc
 gmt grdimage I2_visr.nc -R -J -BweSn -Bp1.0 -Cmycpt.cpt -X6 -Y0 -K -O >> $out_strain
 gmt pscoast -R -J -Wthick,black -Df -Sgray -K -O >> $out_strain
 echo "-122.8 42.3 VISR" | gmt pstext -R -J -F+f18p,Helvetica-Bold -N -K -O >> $out_strain
@@ -44,6 +47,7 @@ gmt psvelo $output_dir"visr/negative_eigs.txt" -Se0.003/0.68/0 -A+b+n10+pthick,b
 # GPSgridder Strain
 gmt grdedit $infile2=gd?HDF5:"$infile2"://I2 -R$range -T -G$"I2_gpsgridder.nc" 
 gmt grdedit I2_gpsgridder.nc -Ev
+gmt grdmath I2_gpsgridder.nc ABS LOG10 = I2_gpsgridder.nc
 gmt grdimage I2_gpsgridder.nc -R -J -BweSn -Bp1.0 -Cmycpt.cpt -X6 -Y0 -K -O >> $out_strain
 gmt pscoast -R -J -Wthick,black -Df -Sgray -K -O >> $out_strain
 echo "-122.8 42.3 gpsgridder" | gmt pstext -R -J -F+f18p,Helvetica-Bold -N -K -O >> $out_strain
@@ -53,7 +57,7 @@ gmt psvelo $output_dir"gpsgridder/negative_eigs.txt" -Se0.003/0.68/0 -A+b+n10+pt
 
 
 # Rotation
-gmt makecpt -T0/300/10 -Cmagma.cpt -Do -G0.30/1.0 > mycpt.cpt
+gmt makecpt -T0/300/10 -Cmagma -Do -G0.30/1.0 > mycpt.cpt
 gmt grdedit $infile1=gd?HDF5:"$infile1"://rotation -R$range -T -G$"rot_delaunay.nc" 
 gmt grdedit rot_delaunay.nc -Ev
 gmt grdimage rot_delaunay.nc -R -J -BWeSn -Bp1.0 -Cmycpt.cpt -X-18 -Y-8 -K -O >> $out_strain

readme.md

@@ -114,8 +114,8 @@ class your_strain_method(strain_2d.Strain_2d):
         return
 
     def compute(self, myVelfield):
-        [Ve, Vn, rot_grd, exx_grd, exy_grd, eyy_grd] = your_strain_method_compute(myVelfield... etc);
-        return [Ve, Vn, rot_grd, exx_grd, exy_grd, eyy_grd];
+        [Ve, Vn, rot_grd, exx_grd, exy_grd, eyy_grd, velfield, residual_velfield] = your_strain_method_compute(myVelfield... etc);
+        return [Ve, Vn, rot_grd, exx_grd, exy_grd, eyy_grd, velfield, residual_velfield];
 ```
 
 where:
@@ -131,9 +131,10 @@ where:
 To reproduce the figure in the README:  
 1. In the example/ directory, run: ```strain_rate_compute.py --print_config``` to print an example config file (similar to the one provided here in the repo).
 2. Run: ```strain_rate_compute.py example_strain_config.txt``` to compute delaunay strain rate using the parameters in the newly-created config file. 
-3. Change the method in the config file to try other methods, and re-run each time for different strain calculations with different parameters.
+3. Change the method in the config file to try other methods, and re-run each time for different strain calculations with different parameters. Try with ```gpsgridder```, ```delaunay```, and ```loc_avg_grad```. If you have the visr executable on your system, try with ```visr``` as well.
 4. Run: ```strain_rate_comparison.py example_strain_config.txt ``` to compute average strain rate maps from several results.
-5. Run: ```Display_output/comparison_rows_example.sh -125/-121/38/42``` to view a GMT plot with several strain rate calculations in Northern California together. 
+5. Navigate into ```Display_output/```
+6. Run: ```./comparison_rows_example.sh -125/-121/38/42``` to view a GMT plot with several strain rate calculations in Northern California together. 
 
 ![strain](https://github.com/kmaterna/2D_Strain/blob/master/example/Display_output/output_rows.png)
 

version.txt

@@ -1 +1 @@
-version="1.1.0"
+version="1.1.1"