Merge remote-tracking branch 'origin/master'

docs/source/examples_simple_2D.rst

@@ -110,7 +110,7 @@ You can now run the model:
 
 .. code-block:: none
 
-    python -m gprMax cylinder_Ascan_2D.in
+    python -m gprMax user_models/cylinder_Ascan_2D.in
 
 View the results
 ----------------
@@ -119,7 +119,7 @@ You should have produced an output file ``cylinder_Ascan_2D.out``. You can view
 
 .. code-block:: none
 
-    python -m tools.plot_Ascan cylinder_Ascan_2D.out
+    python -m tools.plot_Ascan user_models/cylinder_Ascan_2D.out
 
 :numref:`cylinder_Ascan_results` shows the time history of the electric and magnetic field components and currents at the receiver location. The :math:`E_z` field component can be converted to voltage which represents the A-scan (trace). The initial part of the signal (<1.5 ns) represents the direct wave from transmitter to receiver. Then comes the reflected wavelet from the metal cylinder.
 
@@ -148,7 +148,7 @@ To run the model for a B-scan is slightly different than for a single A-scan. Yo
 
 .. code-block:: none
 
-    python -m gprMax cylinder_Bscan_2D.in -n 60
+    python -m gprMax user_models/cylinder_Bscan_2D.in -n 60
 
 
 Results
@@ -158,7 +158,7 @@ You should have produced 60 output files, one for each A-scan, with names ``cyli
 
 .. code-block:: none
 
-    python -m tools.outputfiles_merge cylinder_Bscan_2D 60
+    python -m tools.outputfiles_merge user_models/cylinder_Bscan_2D 60
 
 You should see a combined output file ``cylinder_Bscan_2D_all.out``. The tool will ask you if you want to delete the original single A-scan output files or keep them.
 
@@ -166,7 +166,7 @@ You can now view an image of the B-scan using the command:
 
 .. code-block:: none
 
-    python -m tools.plot_Bscan cylinder_Bscan_2D_all.out --field Ez
+    python -m tools.plot_Bscan user_models/cylinder_Bscan_2D_all.out Ez
 
 :numref:`cylinder_Bscan_results` shows the B-scan (image of the :math:`E_z` field component). As expected a hyperbolic response is present from the metal cylinder.
 

setup.py

@@ -107,7 +107,7 @@ elif sys.platform == 'darwin':
     if gccpath:
         os.environ['CC'] = gccpath[0].split(os.sep)[-1]
     else:
-        raise('Cannot find gcc in /usr/local/bin. gprMax requires gcc to be installed - easily done through the Homebrew package manager (http://brew.sh).')
+        raise('Cannot find gcc in /usr/local/bin. gprMax requires gcc to be installed - easily done through the Homebrew package manager (http://brew.sh). Note: gcc with OpenMP support must be installed')
     compile_args = ['-O3', '-fopenmp', '-w']
     linker_args = ['-fopenmp']
 # Linux

tools/MATLAB scripts/plot_Ascan.m

@@ -16,7 +16,7 @@ if filename ~= 0
     header.dy = tmp(2);
     header.dz = tmp(3);
     header.dt = h5readatt(fullfilename, '/', 'dt');
-    header.ntx = h5readatt(fullfilename, '/', 'ntx');
+    header.nsrc = h5readatt(fullfilename, '/', 'nsrc');
     header.nrx = h5readatt(fullfilename, '/', 'nrx');
     
     % Time vector for plotting
@@ -35,11 +35,12 @@ if filename ~= 0
     
     % Save and plot fields from each receiver
     for n=1:header.nrx
-        path = strcat('/rxs/rx', num2str(n), '/');
+        path = strcat('/rxs/rx', num2str(n));
-        tmp = h5read(fullfilename, strcat(path, 'Position'));
+        tmp = h5readatt(fullfilename, path, 'Position');
         header.rx(n) = tmp(1);
         header.ry(n) = tmp(2);
         header.rz(n) = tmp(3);
+        path = strcat(path, '/');
         fields.ex(:,n) = h5read(fullfilename, strcat(path, 'Ex'));
         fields.ey(:,n) = h5read(fullfilename, strcat(path, 'Ey'));
         fields.ez(:,n) = h5read(fullfilename, strcat(path, 'Ez'));

tools/plot_Bscan.py

@@ -26,9 +26,9 @@ from gprMax.exceptions import CmdInputError
 """Plots a B-scan image."""
 
 # Parse command line arguments
-parser = argparse.ArgumentParser(description='Plots a B-scan image.', usage='cd gprMax; python -m tools.plot_Bscan outputfile --field fieldcomponent')
+parser = argparse.ArgumentParser(description='Plots a B-scan image.', usage='cd gprMax; python -m tools.plot_Bscan outputfile output')
 parser.add_argument('outputfile', help='name of output file including path')
-parser.add_argument('--output', help='name of output to be plotted, i.e. Ex Ey Ez')
+parser.add_argument('output', help='name of output to be plotted, i.e. Ex Ey Ez')
 args = parser.parse_args()
 
 # Open output file and read some attributes
@@ -37,11 +37,10 @@ path = '/rxs/rx1'
 availablecomponents = list(f[path].keys())
 
 # Check if requested output is in file
-if args.output[0] not in availablecomponents:
+if args.output not in availablecomponents:
-    raise CmdInputError('{} output requested to plot, but the available output for receiver 1 is {}'.format(args.outputs[0], ', '.join(availablecomponents)))
+    raise CmdInputError('{} output requested to plot, but the available output for receiver 1 is {}'.format(args.output, ', '.join(availablecomponents)))
 
 outputdata = f[path + '/' + args.output]
-f.close()
 
 # Check that there is more than one A-scan present
 if outputdata.shape[1] == 1:
@@ -61,9 +60,10 @@ elif 'H' in args.output:
 elif 'I' in args.output:
     cb.set_label('Current [A]')
 
-plt.show()
-
 # Save a PDF/PNG of the figure
 #fig.savefig(os.path.splitext(os.path.abspath(file))[0] + '.pdf', dpi=None, format='pdf', bbox_inches='tight', pad_inches=0.1)
 #fig.savefig(os.path.splitext(os.path.abspath(file))[0] + '.png', dpi=150, format='png', bbox_inches='tight', pad_inches=0.1)
 
+plt.show()
+f.close()
+