Merge branch 'master' of https://github.com/gprMax/gprMax

xdmf and hdf5 geometry

tools/plot_Bscan.py

@@ -24,55 +24,75 @@ import matplotlib.pyplot as plt
 from gprMax.exceptions import CmdInputError
 
 
-def make_plot(filename, output):
-    """Plots a B-scan image.
+def get_output_data(filename, rxnumber, rxcomponent):
+    """Gets B-scan output data from a model.
         
-        Args:
+    Args:
         filename (string): Filename (including path) of output file.
-        output (string): Field/current component to plot.
+        rxnumber (int): Receiver output number.
+        rxcomponent (str): Receiver output field/current component.
+        
+    Returns:
+        outputdata (array): Array of A-scans, i.e. B-scan data.
+        dt (float): Temporal resolution of the model.
     """
 
     # Open output file and read some attributes
     f = h5py.File(filename, 'r')
     nrx = f.attrs['nrx']
+    dt = f.attrs['dt']
 
     # Check there are any receivers
     if nrx == 0:
         raise CmdInputError('No receivers found in {}'.format(filename))
 
-    for rx in range(1, nrx + 1):
-        path = '/rxs/rx' + str(rx) + '/'
-        availableoutputs = list(f[path].keys())
+    path = '/rxs/rx' + str(rxnumber) + '/'
+    availableoutputs = list(f[path].keys())
 
-        # Check if requested output is in file
-        if output not in availableoutputs:
-            raise CmdInputError('{} output requested to plot, but the available output for receiver 1 is {}'.format(output, ', '.join(availableoutputs)))
+    # Check if requested output is in file
+    if rxcomponent not in availableoutputs:
+        raise CmdInputError('{} output requested to plot, but the available output for receiver 1 is {}'.format(rxcomponent, ', '.join(availableoutputs)))
 
-        outputdata = f[path + '/' + output]
+    outputdata = f[path + '/' + rxcomponent]
+    outputdata = np.array(outputdata)
 
-        # Check that there is more than one A-scan present
-        if outputdata.shape[1] == 1:
-            raise CmdInputError('{} contains only a single A-scan.'.format(filename))
+    # Check that there is more than one A-scan present
+    if outputdata.shape[1] == 1:
+        raise CmdInputError('{} contains only a single A-scan.'.format(filename))
 
-        # Plot B-scan image
-        fig = plt.figure(num='rx' + str(rx), figsize=(20, 10), facecolor='w', edgecolor='w')
-        plt.imshow(outputdata, extent=[0, outputdata.shape[1], outputdata.shape[0]*f.attrs['dt'], 0], interpolation='nearest', aspect='auto', cmap='seismic', vmin=-np.amax(np.abs(outputdata)), vmax=np.amax(np.abs(outputdata)))
-        plt.xlabel('Trace number')
-        plt.ylabel('Time [s]')
-        plt.grid()
-        cb = plt.colorbar()
-        if 'E' in args.output:
-            cb.set_label('Field strength [V/m]')
-        elif 'H' in args.output:
-            cb.set_label('Field strength [A/m]')
-        elif 'I' in args.output:
-            cb.set_label('Current [A]')
+    return outputdata, dt
 
-        # Save a PDF/PNG of the figure
-        #fig.savefig(os.path.splitext(os.path.abspath(args.outputfile))[0] + '.pdf', dpi=None, format='pdf', bbox_inches='tight', pad_inches=0.1)
-        #fig.savefig(os.path.splitext(os.path.abspath(args.outputfile))[0] + '.png', dpi=150, format='png', bbox_inches='tight', pad_inches=0.1)
+def mpl_plot(outputdata, dt, rxnumber, rxcomponent):
+    """Creates a plot (with matplotlib) of the B-scan.
+        
+    Args:
+        outputdata (array): Array of A-scans, i.e. B-scan data.
+        dt (float): Temporal resolution of the model.
+        rxnumber (int): Receiver output number.
+        rxcomponent (str): Receiver output field/current component.
+        
+    Returns:
+        plt (object): matplotlib plot object.
+    """
 
-    plt.show()
+    fig = plt.figure(num='rx' + str(rxnumber), figsize=(20, 10), facecolor='w', edgecolor='w')
+    plt.imshow(outputdata, extent=[0, outputdata.shape[1], outputdata.shape[0]*dt, 0], interpolation='nearest', aspect='auto', cmap='seismic', vmin=-np.amax(np.abs(outputdata)), vmax=np.amax(np.abs(outputdata)))
+    plt.xlabel('Trace number')
+    plt.ylabel('Time [s]')
+    plt.grid()
+    cb = plt.colorbar()
+    if 'E' in rxcomponent:
+        cb.set_label('Field strength [V/m]')
+    elif 'H' in rxcomponent:
+        cb.set_label('Field strength [A/m]')
+    elif 'I' in rxcomponent:
+        cb.set_label('Current [A]')
+
+    # Save a PDF/PNG of the figure
+    #fig.savefig('Bscan' + str(rxnumber) + '.pdf', dpi=None, format='pdf', bbox_inches='tight', pad_inches=0.1)
+    #fig.savefig('Bscan' + str(rxnumber) + '.png', dpi=150, format='png', bbox_inches='tight', pad_inches=0.1)
+
+    return plt
 
 
 if __name__ == "__main__":
@@ -80,7 +100,20 @@ if __name__ == "__main__":
     # Parse command line arguments
     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 component to be plotted', choices=['Ex', 'Ey', 'Ez', 'Hx', 'Hy', 'Hz', 'Ix', 'Iy', 'Iz'])
+    parser.add_argument('rx_component', help='name of output component to be plotted', choices=['Ex', 'Ey', 'Ez', 'Hx', 'Hy', 'Hz', 'Ix', 'Iy', 'Iz'])
     args = parser.parse_args()
 
-    make_plot(args.outputfile, args.output)
+    # Open output file and read number of outputs (receivers)
+    f = h5py.File(args.outputfile, 'r')
+    nrx = f.attrs['nrx']
+    f.close()
+
+    # Check there are any receivers
+    if nrx == 0:
+        raise CmdInputError('No receivers found in {}'.format(args.outputfile))
+
+    for rx in range(1, nrx + 1):
+        outputdata, dt = get_output_data(args.outputfile, rx, args.rx_component)
+        plt = mpl_plot(outputdata, dt, rx, args.rx_component)
+
+    plt.show()

tools/plot_antenna_params.py

@@ -25,14 +25,14 @@ import matplotlib.gridspec as gridspec
 from gprMax.exceptions import CmdInputError
 
 
-def plot_antenna_params(filename, tln=1, rxn=None, rx=None):
+def plot_antenna_params(filename, tlnumber=1, rxnumber=None, rxcomponent=None):
     """Calculates and plots antenna parameters - s11, (s21) and input impedance.
             
     Args:
         filename (string): Filename (including path) of output file.
-        tln (int): Transmitting antenna - transmission line number
-        rxn (int): Receiver antenna - output number
-        rx (str): Receiver antenna - output electric field component
+        tlnumber (int): Transmitting antenna - transmission line number
+        rxnumber (int): Receiver antenna - output number
+        rxcomponent (str): Receiver antenna - output electric field component
     """
 
     # Open output file and read some attributes
@@ -51,7 +51,7 @@ def plot_antenna_params(filename, tln=1, rxn=None, rx=None):
     print('Frequency bin spacing: {:g} Hz'.format(df))
 
     # Read/calculate voltages and currents
-    tlpath = '/tls/tl' + str(tln) + '/'
+    tlpath = '/tls/tl' + str(tlnumber) + '/'
 
     # Incident voltages/currents
     Vinc = f[tlpath + 'Vinc'][:]
@@ -66,24 +66,21 @@ def plot_antenna_params(filename, tln=1, rxn=None, rx=None):
     Iref = Itotal - Iinc
 
     # If a receiver number for a receiever antenna is given can get received voltage for s21
-    if rxn:
-        if rx not in ['Ex', 'Ey', 'Ez']:
-            raise CmdInputError('The field component for the receiver antenna output must be Ex, Ey, or Ez')
-        
-        rxpath = '/rxs/rx' + str(rxn) + '/'
+    if rxnumber:       
+        rxpath = '/rxs/rx' + str(rxnumber) + '/'
         availableoutputs = list(f[rxpath].keys())
         
-        if rx not in availableoutputs:
-            raise CmdInputError('{} output requested, but the available output for receiver {} is {}'.format(rx, rxn, ', '.join(availableoutputs)))
+        if rxcomponent not in availableoutputs:
+            raise CmdInputError('{} output requested, but the available output for receiver {} is {}'.format(rxcomponent, rxnumber, ', '.join(availableoutputs)))
         
-        rxpath += rx
+        rxpath += rxcomponent
         
         # Received voltage
-        if rx == 'Ex':
+        if rxcomponent == 'Ex':
             Vrec = f[rxpath][:] * -1 * dxdydz[0]
-        elif rx == 'Ey':
+        elif rxcomponent == 'Ey':
             Vrec = f[rxpath][:] * -1 * dxdydz[1]
-        elif rx == 'Ez':
+        elif rxcomponent == 'Ez':
             Vrec = f[rxpath][:] * -1 * dxdydz[2]
     f.close()
 
@@ -95,7 +92,7 @@ def plot_antenna_params(filename, tln=1, rxn=None, rx=None):
 
     # Calculate s11
     s11 = np.abs(np.fft.fft(Vref) * delaycorrection) / np.abs(np.fft.fft(Vinc) * delaycorrection)
-    if rxn:
+    if rxnumber:
         s21 = np.abs(np.fft.fft(Vrec)) / np.abs(np.fft.fft(Vinc) * delaycorrection)
 
     # Calculate input impedance
@@ -112,7 +109,7 @@ def plot_antenna_params(filename, tln=1, rxn=None, rx=None):
     Vtotalp = 20 * np.log10(np.abs((np.fft.fft(Vtotal) * delaycorrection)))
     Itotalp = 20 * np.log10(np.abs(np.fft.fft(Itotal)))
     s11 = 20 * np.log10(s11)
-    if rxn:
+    if rxnumber:
         s21 = 20 * np.log10(s21)
 
     # Set plotting range
@@ -278,7 +275,7 @@ def plot_antenna_params(filename, tln=1, rxn=None, rx=None):
     ax.grid()
 
     # Plot frequency spectra of s21
-    if rxn:
+    if rxnumber:
         ax = plt.subplot(gs2[0, 1])
         markerline, stemlines, baseline = ax.stem(freqs[pltrange], s21[pltrange], '-.')
         plt.setp(baseline, 'linewidth', 0)
@@ -363,10 +360,10 @@ if __name__ == "__main__":
     # Parse command line arguments
     parser = argparse.ArgumentParser(description='Plots antenna parameters (s11, s21 parameters and input impedance) from an output file containing a transmission line source.', usage='cd gprMax; python -m tools.plot_antenna_params outputfile')
     parser.add_argument('outputfile', help='name of output file including path')
-    parser.add_argument('-tln', default=1, type=int, help='transmitting antenna - transmission line number')
-    parser.add_argument('-rxn', type=int, help='receiver antenna - output number')
-    parser.add_argument('-rx', type=str, help='receiver antenna - output electric field component')
+    parser.add_argument('--tl-num', default=1, type=int, help='transmitting antenna - transmission line number')
+    parser.add_argument('--rx-num', type=int, help='receiver antenna - output number')
+    parser.add_argument('--rx-component', type=str, help='receiver antenna - output electric field component', choices=['Ex', 'Ey', 'Ez'])
     args = parser.parse_args()
 
-    plot_antenna_params(args.outputfile, args.tln, args.rxn, args.rx)
+    plot_antenna_params(args.outputfile, args.tl_num, args.rx_num, args.rx_component)