Change HDF5 file attribute from 'dx,dy,dz' to 'dx_dy_dz'

tools/MATLAB_scripts/plot_Ascan.m

@@ -11,17 +11,17 @@ fullfilename = strcat(pathname, filename);
 if filename ~= 0
     header.title = h5readatt(fullfilename, '/', 'Title');
     header.iterations = double(h5readatt(fullfilename,'/', 'Iterations'));
-    tmp = h5readatt(fullfilename, '/', 'dx, dy, dz');
+    tmp = h5readatt(fullfilename, '/', 'dx_dy_dz');
     header.dx = tmp(1);
     header.dy = tmp(2);
     header.dz = tmp(3);
     header.dt = h5readatt(fullfilename, '/', 'dt');
     header.nsrc = h5readatt(fullfilename, '/', 'nsrc');
     header.nrx = h5readatt(fullfilename, '/', 'nrx');
-    
+
     % Time vector for plotting
     time = linspace(0, (header.iterations)*(header.dt), header.iterations)';
-    
+
     % Initialise structure for field arrays
     fields.ex = zeros(header.iterations, header.nrx);
     fields.ey = zeros(header.iterations, header.nrx);
@@ -29,7 +29,7 @@ if filename ~= 0
     fields.hx = zeros(header.iterations, header.nrx);
     fields.hy = zeros(header.iterations, header.nrx);
     fields.hz = zeros(header.iterations, header.nrx);
-    
+
     % Save and plot fields from each receiver
     for n=1:header.nrx
         path = strcat('/rxs/rx', num2str(n));
@@ -44,7 +44,7 @@ if filename ~= 0
         fields.hx(:,n) = h5read(fullfilename, strcat(path, 'Hx'));
         fields.hy(:,n) = h5read(fullfilename, strcat(path, 'Hy'));
         fields.hz(:,n) = h5read(fullfilename, strcat(path, 'Hz'));
-        
+
         fh1=figure('Name', strcat('rx', num2str(n)));
         ax(1) = subplot(3,2,1); plot(time, fields.ex(:,n), 'r', 'LineWidth', 2), grid on, xlabel('Time [s]'), ylabel('Field strength [V/m]'), title('E_x')
         ax(2) = subplot(3,2,3); plot(time, fields.ey(:,n), 'r', 'LineWidth', 2), grid on, xlabel('Time [s]'), ylabel('Field strength [V/m]'), title('E_y')
@@ -53,7 +53,7 @@ if filename ~= 0
         ax(5) = subplot(3,2,4); plot(time, fields.hy(:,n), 'b', 'LineWidth', 2), grid on, xlabel('Time [s]'), ylabel('Field strength [A/m]'), title('H_y')
         ax(6) = subplot(3,2,6); plot(time, fields.hz(:,n), 'b', 'LineWidth', 2), grid on, xlabel('Time [s]'), ylabel('Field strength [A/m]'), title('H_z')
         set(ax,'FontSize', 16, 'xlim', [0 time(end)]);
-        
+
         % Options to create a nice looking figure for display and printing
         set(fh1,'Color','white','Menubar','none');
         X = 60;   % Paper size
@@ -62,11 +62,11 @@ if filename ~= 0
         yMargin = 0;  % Bottom/top margins from page borders
         xSize = X - 2*xMargin;    % Figure size on paper (width & height)
         ySize = Y - 2*yMargin;    % Figure size on paper (width & height)
-        
+
         % Figure size displayed on screen
         set(fh1, 'Units','centimeters', 'Position', [0 0 xSize ySize])
         movegui(fh1, 'center')
-        
+
         % Figure size printed on paper
         set(fh1,'PaperUnits', 'centimeters')
         set(fh1,'PaperSize', [X Y])

tools/convert_png2h5.py

@@ -72,7 +72,7 @@ def pixel_match(pixellist, pixeltest):
 
 
 if __name__ == "__main__":
-    
+
     # Parse command line arguments
     parser = argparse.ArgumentParser(description='Convert a PNG image to a HDF5 file that can be used to import geometry (#geometry_objects_read) into a 2D gprMax model. Colours from the image are selected which correspond to a list of materials that should be supplied in a separate text file.', usage='python convert_png2h5.py imagefile dx dy dz')
     parser.add_argument('imagefile', help='name of image file including path')
@@ -82,7 +82,7 @@ if __name__ == "__main__":
 
     # Open image file
     im = mpimg.imread(args.imagefile)
-    
+
     # Store image data to use for creating geometry
     imdata = np.rot90(im, k=3) # Rotate 90CW
     imdata = np.floor(imdata * 255).astype(np.int16) # Convert pixel values from float (0-1) to integer (0-255)
@@ -101,25 +101,25 @@ if __name__ == "__main__":
     plt.show()
 
     # Format spatial resolution into tuple
-    dxdydz = (args.dxdydz[0][0], args.dxdydz[0][1], args.dxdydz[0][2])
-    
+    dx_dy_dz = (args.dxdydz[0][0], args.dxdydz[0][1], args.dxdydz[0][2])
+
     # Filename for geometry (HDF5) file
     hdf5file = os.path.splitext(args.imagefile)[0] + '.h5'
-    
+
     # Array to store geometry data (initialised as background, i.e. -1)
     data = np.ones((imdata.shape[0], imdata.shape[1], args.zcells), dtype=np.int16) * -1
 
     # Write geometry (HDF5) file
     with h5py.File(hdf5file, 'w') as fout:
 
-        # Add attribute with name 'dx, dy, dz' for spatial resolution
-        fout.attrs['dx, dy, dz'] = dxdydz
+        # Add attribute with name 'dx_dy_dz' for spatial resolution
+        fout.attrs['dx_dy_dz'] = dx_dy_dz
 
         # Use a boolean mask to match selected pixel values with position in image
         for i, material in enumerate(materials):
             mask = np.all(imdata == material, axis=-1)
             data[mask,:] = i
-        
+
         # Write data to file
         fout.create_dataset('data', data=data)
 

tools/plot_antenna_params.py

@@ -44,7 +44,7 @@ def calculate_antenna_params(filename, tltxnumber=1, tlrxnumber=None, rxnumber=N
 
     # Open output file and read some attributes
     f = h5py.File(filename, 'r')
-    dxdydz = f.attrs['dx, dy, dz']
+    dxdydz = f.attrs['dx_dy_dz']
     dt = f.attrs['dt']
     iterations = f.attrs['Iterations']