Formatting cleanups.

user_libs/AustinManWoman/head_only_hdf5.py

@@ -1,4 +1,6 @@
-import argparse, os
+import argparse
+import os
+
 import h5py
 
 # Parse command line arguments
@@ -6,18 +8,18 @@ parser = argparse.ArgumentParser(description='Writes a HDF5 file of AustinMan or
 parser.add_argument('filename', help='name and path to (HDF5) file containing AustinMan or AustinWoman model')
 args = parser.parse_args()
 
-# Read full body HDF5 file         
+# Read full body HDF5 file
 f = h5py.File(args.filename, 'r')
 dx_dy_dz = f.attrs['dx, dy, dz']
-data = f['/data'][:,:,:]
+data = f['/data'][:, :, :]
 
 # Define head as last 1/8 of total body height
 nzhead = 7 * int(data.shape[2] / 8)
 
 print('Dimensions of head model: {:g} x {:g} x {:g} cells'.format(data.shape[0], data.shape[1], data.shape[2] - nzhead))
-    
+
 # Write HDF5 file
 headfile = os.path.splitext(args.filename)[0] + '_head.h5'
 f = h5py.File(headfile, 'w')
 f.attrs['dx, dy, dz'] = dx_dy_dz
-f['/data'] = data[:,:,nzhead:data.shape[2]]
+f['/data'] = data[:, :, nzhead:data.shape[2]]

user_libs/antenna_patterns/initial_save.py

@@ -36,37 +36,37 @@ epsr = 5
 
 # Observation radii and angles
 radii = np.linspace(0.1, 0.3, 20)
-theta = np.linspace(3, 357, 60) * (180/np.pi)
+theta = np.linspace(3, 357, 60) * (180 / np.pi)
 
 # Scaling of time-domain field pattern values by material impedance
 impscaling = False
 
 # Centre frequency of modelled antenna
-f = 1.5e9 # GSSI 1.5GHz antenna model
+f = 1.5e9  # GSSI 1.5GHz antenna model
 
 # Largest dimension of antenna transmitting element
-D = 0.060 # GSSI 1.5GHz antenna model
+D = 0.060  # GSSI 1.5GHz antenna model
 
 # Traces to plot for sanity checking
-traceno = np.s_[:] # All traces
+traceno = np.s_[:]  # All traces
 ########################################
 
 # Critical angle and velocity
 if epsr:
     mr = 1
-    z1 = np.sqrt(mr/epsr) * z0
+    z1 = np.sqrt(mr / epsr) * z0
     v1 = c / np.sqrt(epsr)
-    thetac = np.round(np.arcsin(v1/c) * (180/np.pi))
-    wavelength = v1/f
+    thetac = np.round(np.arcsin(v1 / c) * (180 / np.pi))
+    wavelength = v1 / f
 
 # Print some useful information
-print('Centre frequency: {} GHz'.format(f/1e9))
+print('Centre frequency: {} GHz'.format(f / 1e9))
 if epsr:
     print('Critical angle for Er {} is {} degrees'.format(epsr, thetac))
     print('Wavelength: {:.3f} m'.format(wavelength))
-    print('Observation distance(s) from {:.3f} m ({:.1f} wavelengths) to {:.3f} m ({:.1f} wavelengths)'.format(radii[0], radii[0]/wavelength, radii[-1], radii[-1]/wavelength))
-    print('Theoretical boundary between reactive & radiating near-field (0.62*sqrt((D^3/wavelength): {:.3f} m'.format(0.62 * np.sqrt((D**3)/wavelength)))
-    print('Theoretical boundary between radiating near-field & far-field (2*D^2/wavelength): {:.3f} m'.format((2 * D**2)/wavelength))
+    print('Observation distance(s) from {:.3f} m ({:.1f} wavelengths) to {:.3f} m ({:.1f} wavelengths)'.format(radii[0], radii[0] / wavelength, radii[-1], radii[-1] / wavelength))
+    print('Theoretical boundary between reactive & radiating near-field (0.62*sqrt((D^3/wavelength): {:.3f} m'.format(0.62 * np.sqrt((D**3) / wavelength)))
+    print('Theoretical boundary between radiating near-field & far-field (2*D^2/wavelength): {:.3f} m'.format((2 * D**2) / wavelength))
 
 # Load text file with coordinates of pattern origin
 origin = np.loadtxt(os.path.splitext(outputfile)[0] + '_rxsorigin.txt')
@@ -77,13 +77,13 @@ iterations = f.attrs['Iterations']
 dt = f.attrs['dt']
 nrx = f.attrs['nrx']
 if antenna:
-    nrx = nrx - 1 # Ignore first receiver point with full antenna model
+    nrx = nrx - 1  # Ignore first receiver point with full antenna model
     start = 2
 else:
     start = 1
 time = np.arange(0, dt * iterations, dt)
 time = time / 1E-9
-fs = 1 / dt # Sampling frequency
+fs = 1 / dt  # Sampling frequency
 
 # Initialise arrays to store fields
 coords = np.zeros((nrx, 3), dtype=np.float32)
@@ -115,7 +115,7 @@ for rx in range(0, nrx):
     Hz[:, rx] = f[path + 'Hz'][:]
 f.close()
 
-## Plot traces for sanity checking
+# Plot traces for sanity checking
 #fig, ((ax1, ax2), (ax3, ax4), (ax5, ax6)) = plt.subplots(num=outputfile, nrows=3, ncols=2, sharex=False, sharey='col', subplot_kw=dict(xlabel='Time [ns]'), figsize=(20, 10), facecolor='w', edgecolor='w')
 #ax1.plot(time, Ex[:, traceno],'r', lw=2)
 #ax1.set_ylabel('$E_x$, field strength [V/m]')
@@ -129,12 +129,12 @@ f.close()
 #ax4.set_ylabel('$H_y$, field strength [A/m]')
 #ax6.plot(time, Hz[:, traceno],'b', lw=2)
 #ax6.set_ylabel('$H_z$, field strength [A/m]')
-## Turn on grid
+# Turn on grid
 #[ax.grid() for ax in fig.axes]
-#plt.show()
+# plt.show()
 
 # Calculate fields for patterns
-rxstart = 0 # Index for rx points
+rxstart = 0  # Index for rx points
 for radius in range(0, len(radii)):
     index = 0
     # Observation points

user_libs/antenna_patterns/plot_fields.py

@@ -35,13 +35,13 @@ epsr = 5
 # Observation radii and angles
 radii = np.linspace(0.1, 0.3, 20)
 theta = np.linspace(3, 357, 60)
-theta = np.deg2rad(np.append(theta, theta[0])) # Append start value to close circle
+theta = np.deg2rad(np.append(theta, theta[0]))  # Append start value to close circle
 
 # Centre frequency of modelled antenna
-f = 1.5e9 # GSSI 1.5GHz antenna model
+f = 1.5e9  # GSSI 1.5GHz antenna model
 
 # Largest dimension of antenna transmitting element
-D = 0.060 # GSSI 1.5GHz antenna model
+D = 0.060  # GSSI 1.5GHz antenna model
 
 # Minimum value for plotting energy and ring steps (dB)
 min = -72
@@ -51,19 +51,19 @@ step = 12
 # Critical angle and velocity
 if epsr:
     mr = 1
-    z1 = np.sqrt(mr/epsr) * z0
+    z1 = np.sqrt(mr / epsr) * z0
     v1 = c / np.sqrt(epsr)
-    thetac = np.round(np.rad2deg(np.arcsin(v1/c)))
-    wavelength = v1/f
+    thetac = np.round(np.rad2deg(np.arcsin(v1 / c)))
+    wavelength = v1 / f
 
 # Print some useful information
-print('Centre frequency: {} GHz'.format(f/1e9))
+print('Centre frequency: {} GHz'.format(f / 1e9))
 if epsr:
     print('Critical angle for Er {} is {} degrees'.format(epsr, thetac))
     print('Wavelength: {:.3f} m'.format(wavelength))
-    print('Observation distance(s) from {:.3f} m ({:.1f} wavelengths) to {:.3f} m ({:.1f} wavelengths)'.format(radii[0], radii[0]/wavelength, radii[-1], radii[-1]/wavelength))
-    print('Theoretical boundary between reactive & radiating near-field (0.62*sqrt((D^3/wavelength): {:.3f} m'.format(0.62 * np.sqrt((D**3)/wavelength)))
-    print('Theoretical boundary between radiating near-field & far-field (2*D^2/wavelength): {:.3f} m'.format((2 * D**2)/wavelength))
+    print('Observation distance(s) from {:.3f} m ({:.1f} wavelengths) to {:.3f} m ({:.1f} wavelengths)'.format(radii[0], radii[0] / wavelength, radii[-1], radii[-1] / wavelength))
+    print('Theoretical boundary between reactive & radiating near-field (0.62*sqrt((D^3/wavelength): {:.3f} m'.format(0.62 * np.sqrt((D**3) / wavelength)))
+    print('Theoretical boundary between radiating near-field & far-field (2*D^2/wavelength): {:.3f} m'.format((2 * D**2) / wavelength))
 
 # Setup figure
 fig = plt.figure(num=args.numpyfile, figsize=(8, 8), facecolor='w', edgecolor='w')
@@ -81,15 +81,15 @@ ax.annotate('Ground', xy=(np.deg2rad(270), 0), xytext=(8, -15), textcoords='offs
 
 # Plot patterns
 for patt in range(0, len(radii)):
-    pattplot = np.append(patterns[patt, :], patterns[patt, 0]) # Append start value to close circle
-    pattplot = pattplot / np.max(np.max(patterns)) # Normalise, based on set of patterns
+    pattplot = np.append(patterns[patt, :], patterns[patt, 0])  # Append start value to close circle
+    pattplot = pattplot / np.max(np.max(patterns))  # Normalise, based on set of patterns
     ax.plot(theta, 10 * np.log10(pattplot), label='{:.2f}m'.format(radii[patt]), marker='.', ms=6, lw=1.5)
 
 # Add Hertzian dipole plot
-#hertzplot1 = np.append(hertzian[0, :], hertzian[0, 0]) # Append start value to close circle
+# hertzplot1 = np.append(hertzian[0, :], hertzian[0, 0]) # Append start value to close circle
 #hertzplot1 = hertzplot1 / np.max(np.max(hertzian))
 #ax.plot(theta, 10 * np.log10(hertzplot1), label='Inf. dipole, 0.1m', color='black', ls='-.', lw=3)
-#hertzplot2 = np.append(hertzian[-1, :], hertzian[-1, 0]) # Append start value to close circle
+# hertzplot2 = np.append(hertzian[-1, :], hertzian[-1, 0]) # Append start value to close circle
 #hertzplot2 = hertzplot2 / np.max(np.max(hertzian))
 #ax.plot(theta, 10 * np.log10(hertzplot2), label='Inf. dipole, 0.58m', color='black', ls='--', lw=3)
 
@@ -103,13 +103,13 @@ ax.set_rmax(0)
 ax.set_rlabel_position(45)
 ax.set_yticks(np.arange(min, step, step))
 yticks = ax.get_yticks().tolist()
-yticks[-1]='0 dB'
+yticks[-1] = '0 dB'
 ax.set_yticklabels(yticks)
 
 # Grid and legend
 ax.grid(True)
 handles, existlabels = ax.get_legend_handles_labels()
-leg = ax.legend([handles[0], handles[-1]], [existlabels[0], existlabels[-1]], ncol=2, loc=(0.27,-0.12), frameon=False) # Plot just first and last legend entries
+leg = ax.legend([handles[0], handles[-1]], [existlabels[0], existlabels[-1]], ncol=2, loc=(0.27, -0.12), frameon=False)  # Plot just first and last legend entries
 #leg = ax.legend([handles[0], handles[-3], handles[-2], handles[-1]], [existlabels[0], existlabels[-3], existlabels[-2], existlabels[-1]], ncol=4, loc=(-0.13,-0.12), frameon=False)
 [legobj.set_linewidth(2) for legobj in leg.legendHandles]
 
@@ -120,4 +120,3 @@ fig.savefig(savename, dpi=None, format='pdf', bbox_inches='tight', pad_inches=0.
 #fig.savefig(savename, dpi=150, format='png', bbox_inches='tight', pad_inches=0.1)
 
 plt.show()
-

user_libs/antennas.py

@@ -12,16 +12,17 @@ from gprMax.input_cmd_funcs import *
 
 moduledirectory = os.path.dirname(os.path.abspath(__file__))
 
+
 def antenna_like_GSSI_1500(x, y, z, resolution=0.001, rotate90=False, **kwargs):
     """Inserts a description of an antenna similar to the GSSI 1.5GHz antenna. Can be used with 1mm (default) or 2mm spatial resolution. The external dimensions of the antenna are 170x108x45mm. One output point is defined between the arms of the receiever bowtie. The bowties are aligned with the y axis so the output is the y component of the electric field.
-        
+
     Args:
         x, y, z (float): Coordinates of a location in the model to insert the antenna. Coordinates are relative to the geometric centre of the antenna in the x-y plane and the bottom of the antenna skid in the z direction.
         resolution (float): Spatial resolution for the antenna model.
         rotate90 (bool): Rotate model 90 degrees CCW in xy plane.
         kwargs (dict): Optional variables, e.g. can be fed from an optimisation process.
     """
-    
+
     # Antenna geometry properties
     casesize = (0.170, 0.108, 0.043)
     casethickness = 0.002
@@ -32,7 +33,7 @@ def antenna_like_GSSI_1500(x, y, z, resolution=0.001, rotate90=False, **kwargs):
     bowtiebase = 0.022
     bowtieheight = 0.014
     patchheight = 0.015
-    
+
     # Set origin for rotation to geometric centre of antenna in x-y plane if required
     if rotate90:
         rotate90origin = (x, y)
@@ -49,25 +50,25 @@ def antenna_like_GSSI_1500(x, y, z, resolution=0.001, rotate90=False, **kwargs):
         absorbersig = kwargs['absorbersig']
         rxres = 50
     else:
-        #excitationfreq = 1.5e9 # GHz
-        #sourceresistance = 50 # Ohms
+        # excitationfreq = 1.5e9 # GHz
+        # sourceresistance = 50 # Ohms
         #absorberEr = 1.7
         #absorbersig = 0.59
-        
+
         # Values from http://hdl.handle.net/1842/4074
         excitationfreq = 1.71e9
         #sourceresistance = 4
-        sourceresistance = 230 # Correction for old (< 123) GprMax3D bug
+        sourceresistance = 230  #  Correction for old (< 123) GprMax3D bug
         absorberEr = 1.58
         absorbersig = 0.428
-        rxres = 925 # Resistance at Rx bowtie
-    
+        rxres = 925  # Resistance at Rx bowtie
+
     x = x - (casesize[0] / 2)
     y = y - (casesize[1] / 2)
-    
+
     # Coordinates of source excitation point in antenna
     tx = x + 0.114, y + 0.053, z + skidthickness
-    
+
     if resolution == 0.001:
         dx = 0.001
         dy = 0.001
@@ -92,43 +93,43 @@ def antenna_like_GSSI_1500(x, y, z, resolution=0.001, rotate90=False, **kwargs):
     # Plastic case
     box(x, y, z + skidthickness, x + casesize[0], y + casesize[1], z + skidthickness + casesize[2], 'hdpe', rotate90origin=rotate90origin)
     box(x + casethickness, y + casethickness, z + skidthickness, x + casesize[0] - casethickness, y + casesize[1] - casethickness, z + skidthickness + casesize[2] - casethickness, 'free_space', rotate90origin=rotate90origin)
-    
+
     # Metallic enclosure
     box(x + 0.025, y + casethickness, z + skidthickness, x + casesize[0] - 0.025, y + casesize[1] - casethickness, z + skidthickness + 0.027, 'pec', rotate90origin=rotate90origin)
-    
+
     # Absorber material, and foam (modelled as PCB material) around edge of absorber
     box(x + 0.025 + shieldthickness, y + casethickness + shieldthickness, z + skidthickness, x + 0.025 + shieldthickness + 0.057, y + casesize[1] - casethickness - shieldthickness, z + skidthickness + 0.027 - shieldthickness - 0.001, 'pcb', rotate90origin=rotate90origin)
     box(x + 0.025 + shieldthickness + foamsurroundthickness, y + casethickness + shieldthickness + foamsurroundthickness, z + skidthickness, x + 0.025 + shieldthickness + 0.057 - foamsurroundthickness, y + casesize[1] - casethickness - shieldthickness - foamsurroundthickness, z + skidthickness + 0.027 - shieldthickness, 'absorber', rotate90origin=rotate90origin)
     box(x + 0.086, y + casethickness + shieldthickness, z + skidthickness, x + 0.086 + 0.057, y + casesize[1] - casethickness - shieldthickness, z + skidthickness + 0.027 - shieldthickness - 0.001, 'pcb', rotate90origin=rotate90origin)
     box(x + 0.086 + foamsurroundthickness, y + casethickness + shieldthickness + foamsurroundthickness, z + skidthickness, x + 0.086 + 0.057 - foamsurroundthickness, y + casesize[1] - casethickness - shieldthickness - foamsurroundthickness, z + skidthickness + 0.027 - shieldthickness, 'absorber', rotate90origin=rotate90origin)
-    
+
     # PCB
     box(x + 0.025 + shieldthickness + foamsurroundthickness, y + casethickness + shieldthickness + foamsurroundthickness, z + skidthickness, x + 0.086 - shieldthickness - foamsurroundthickness, y + casesize[1] - casethickness - shieldthickness - foamsurroundthickness, z + skidthickness + pcbthickness, 'pcb', rotate90origin=rotate90origin)
     box(x + 0.086 + foamsurroundthickness, y + casethickness + shieldthickness + foamsurroundthickness, z + skidthickness, x + 0.086 + 0.057 - foamsurroundthickness, y + casesize[1] - casethickness - shieldthickness - foamsurroundthickness, z + skidthickness + pcbthickness, 'pcb', rotate90origin=rotate90origin)
-    
+
     # PCB components
     if resolution == 0.001:
         # Rx & Tx bowties
         a = 0
         b = 0
         while b < 13:
-            plate(x + 0.045 + a*dx, y + 0.039 + b*dx, z + skidthickness, x + 0.065 - a*dx, y + 0.039 + b*dx + dy, z + skidthickness, 'pec', rotate90origin=rotate90origin)
-            plate(x + 0.045 + a*dx, y + 0.067 - b*dx, z + skidthickness, x + 0.065 - a*dx, y + 0.067 - b*dx + dy, z + skidthickness, 'pec', rotate90origin=rotate90origin)
-            plate(x + 0.104 + a*dx, y + 0.039 + b*dx, z + skidthickness, x + 0.124 - a*dx, y + 0.039 + b*dx + dy, z + skidthickness, 'pec', rotate90origin=rotate90origin)
-            plate(x + 0.104 + a*dx, y + 0.067 - b*dx, z + skidthickness, x + 0.124 - a*dx, y + 0.067 - b*dx + dy, z + skidthickness, 'pec', rotate90origin=rotate90origin)
+            plate(x + 0.045 + a * dx, y + 0.039 + b * dx, z + skidthickness, x + 0.065 - a * dx, y + 0.039 + b * dx + dy, z + skidthickness, 'pec', rotate90origin=rotate90origin)
+            plate(x + 0.045 + a * dx, y + 0.067 - b * dx, z + skidthickness, x + 0.065 - a * dx, y + 0.067 - b * dx + dy, z + skidthickness, 'pec', rotate90origin=rotate90origin)
+            plate(x + 0.104 + a * dx, y + 0.039 + b * dx, z + skidthickness, x + 0.124 - a * dx, y + 0.039 + b * dx + dy, z + skidthickness, 'pec', rotate90origin=rotate90origin)
+            plate(x + 0.104 + a * dx, y + 0.067 - b * dx, z + skidthickness, x + 0.124 - a * dx, y + 0.067 - b * dx + dy, z + skidthickness, 'pec', rotate90origin=rotate90origin)
             b += 1
             if a == 2 or a == 4 or a == 7:
-                plate(x + 0.045 + a*dx, y + 0.039 + b*dx, z + skidthickness, x + 0.065 - a*dx, y + 0.039 + b*dx + dy, z + skidthickness, 'pec', rotate90origin=rotate90origin)
-                plate(x + 0.045 + a*dx, y + 0.067 - b*dx, z + skidthickness, x + 0.065 - a*dx, y + 0.067 - b*dx + dy, z + skidthickness, 'pec', rotate90origin=rotate90origin)
-                plate(x + 0.104 + a*dx, y + 0.039 + b*dx, z + skidthickness, x + 0.124 - a*dx, y + 0.039 + b*dx + dy, z + skidthickness, 'pec', rotate90origin=rotate90origin)
-                plate(x + 0.104 + a*dx, y + 0.067 - b*dx, z + skidthickness, x + 0.124 - a*dx, y + 0.067 - b*dx + dy, z + skidthickness, 'pec', rotate90origin=rotate90origin)
+                plate(x + 0.045 + a * dx, y + 0.039 + b * dx, z + skidthickness, x + 0.065 - a * dx, y + 0.039 + b * dx + dy, z + skidthickness, 'pec', rotate90origin=rotate90origin)
+                plate(x + 0.045 + a * dx, y + 0.067 - b * dx, z + skidthickness, x + 0.065 - a * dx, y + 0.067 - b * dx + dy, z + skidthickness, 'pec', rotate90origin=rotate90origin)
+                plate(x + 0.104 + a * dx, y + 0.039 + b * dx, z + skidthickness, x + 0.124 - a * dx, y + 0.039 + b * dx + dy, z + skidthickness, 'pec', rotate90origin=rotate90origin)
+                plate(x + 0.104 + a * dx, y + 0.067 - b * dx, z + skidthickness, x + 0.124 - a * dx, y + 0.067 - b * dx + dy, z + skidthickness, 'pec', rotate90origin=rotate90origin)
                 b += 1
             a += 1
         # Rx extension section (upper y)
         plate(x + 0.044, y + 0.068, z + skidthickness, x + 0.044 + bowtiebase, y + 0.068 + patchheight, z + skidthickness, 'pec', rotate90origin=rotate90origin)
         # Tx extension section (upper y)
         plate(x + 0.103, y + 0.068, z + skidthickness, x + 0.103 + bowtiebase, y + 0.068 + patchheight, z + skidthickness, 'pec', rotate90origin=rotate90origin)
-        
+
         # Edges that represent wire between bowtie halves in 1mm model
         edge(tx[0] - 0.059, tx[1] - dy, tx[2], tx[0] - 0.059, tx[1], tx[2], 'pec', rotate90origin=rotate90origin)
         edge(tx[0] - 0.059, tx[1] + dy, tx[2], tx[0] - 0.059, tx[1] + 0.002, tx[2], 'pec', rotate90origin=rotate90origin)
@@ -136,12 +137,12 @@ def antenna_like_GSSI_1500(x, y, z, resolution=0.001, rotate90=False, **kwargs):
         edge(tx[0], tx[1] + dz, tx[2], tx[0], tx[1] + 0.002, tx[2], 'pec', rotate90origin=rotate90origin)
 
     elif resolution == 0.002:
-    # Rx & Tx bowties
-        for a in range(0,6):
-            plate(x + 0.044 + a*dx, y + 0.040 + a*dx, z + skidthickness, x + 0.066 - a*dx, y + 0.040 + a*dx + dy, z + skidthickness, 'pec', rotate90origin=rotate90origin)
-            plate(x + 0.044 + a*dx, y + 0.064 - a*dx, z + skidthickness, x + 0.066 - a*dx, y + 0.064 - a*dx + dy, z + skidthickness, 'pec', rotate90origin=rotate90origin)
-            plate(x + 0.103 + a*dx, y + 0.040 + a*dx, z + skidthickness, x + 0.125 - a*dx, y + 0.040 + a*dx + dy, z + skidthickness, 'pec', rotate90origin=rotate90origin)
-            plate(x + 0.103 + a*dx, y + 0.064 - a*dx, z + skidthickness, x + 0.125 - a*dx, y + 0.064 - a*dx + dy, z + skidthickness, 'pec', rotate90origin=rotate90origin)
+        # Rx & Tx bowties
+        for a in range(0, 6):
+            plate(x + 0.044 + a * dx, y + 0.040 + a * dx, z + skidthickness, x + 0.066 - a * dx, y + 0.040 + a * dx + dy, z + skidthickness, 'pec', rotate90origin=rotate90origin)
+            plate(x + 0.044 + a * dx, y + 0.064 - a * dx, z + skidthickness, x + 0.066 - a * dx, y + 0.064 - a * dx + dy, z + skidthickness, 'pec', rotate90origin=rotate90origin)
+            plate(x + 0.103 + a * dx, y + 0.040 + a * dx, z + skidthickness, x + 0.125 - a * dx, y + 0.040 + a * dx + dy, z + skidthickness, 'pec', rotate90origin=rotate90origin)
+            plate(x + 0.103 + a * dx, y + 0.064 - a * dx, z + skidthickness, x + 0.125 - a * dx, y + 0.064 - a * dx + dy, z + skidthickness, 'pec', rotate90origin=rotate90origin)
             # Rx extension section (upper y)
             plate(x + 0.044, y + 0.066, z + skidthickness, x + 0.044 + bowtiebase, y + 0.066 + patchheight, z + skidthickness, 'pec', rotate90origin=rotate90origin)
             # Tx extension section (upper y)
@@ -154,19 +155,19 @@ def antenna_like_GSSI_1500(x, y, z, resolution=0.001, rotate90=False, **kwargs):
 
     # Skid
     box(x, y, z, x + casesize[0], y + casesize[1], z + skidthickness, 'hdpe', rotate90origin=rotate90origin)
-    
+
     # Geometry views
     #geometry_view(x - dx, y - dy, z - dz, x + casesize[0] + dx, y + casesize[1] + dy, z + skidthickness + casesize[2] + dz, dx, dy, dz, 'antenna_like_GSSI_1500')
     #geometry_view(x, y, z, x + casesize[0], y + casesize[1], z + 0.010, dx, dy, dz, 'antenna_like_GSSI_1500_pcb', type='f')
-    
+
     # Excitation - custom pulse
-    #print('#excitation_file: {}'.format(os.path.join(moduledirectory, 'GSSIgausspulse1.txt')))
-    #print('#transmission_line: y {} {} {} {} GSSIgausspulse1'.format(tx[0], tx[1], tx[2], sourceresistance))
+    # print('#excitation_file: {}'.format(os.path.join(moduledirectory, 'GSSIgausspulse1.txt')))
+    # print('#transmission_line: y {} {} {} {} GSSIgausspulse1'.format(tx[0], tx[1], tx[2], sourceresistance))
 
     # Excitation - Gaussian pulse
     print('#waveform: gaussian 1 {} myGaussian'.format(excitationfreq))
     transmission_line('y', tx[0], tx[1], tx[2], sourceresistance, 'myGaussian', dxdy=(resolution, resolution), rotate90origin=rotate90origin)
-    
+
     # Output point - receiver bowtie
     if resolution == 0.001:
         edge(tx[0] - 0.059, tx[1], tx[2], tx[0] - 0.059, tx[1] + dy, tx[2], 'rxres', rotate90origin=rotate90origin)
@@ -178,25 +179,25 @@ def antenna_like_GSSI_1500(x, y, z, resolution=0.001, rotate90=False, **kwargs):
 
 def antenna_like_MALA_1200(x, y, z, resolution=0.001, rotate90=False, **kwargs):
     """Inserts a description of an antenna similar to the MALA 1.2GHz antenna. Can be used with 1mm (default) or 2mm spatial resolution. The external dimensions of the antenna are 184x109x46mm. One output point is defined between the arms of the receiever bowtie. The bowties are aligned with the y axis so the output is the y component of the electric field.
-        
+
     Args:
         x, y, z (float): Coordinates of a location in the model to insert the antenna. Coordinates are relative to the geometric centre of the antenna in the x-y plane and the bottom of the antenna skid in the z direction.
         resolution (float): Spatial resolution for the antenna model.
         rotate90 (bool): Rotate model 90 degrees CCW in xy plane.
         kwargs (dict): Optional variables, e.g. can be fed from an optimisation process.
     """
-    
+
     # Antenna geometry properties
     casesize = (0.184, 0.109, 0.040)
     casethickness = 0.002
     cavitysize = (0.062, 0.062, 0.037)
     cavitythickness = 0.001
     pcbthickness = 0.002
-    polypropylenethickness = 0.003;
-    hdpethickness = 0.003;
+    polypropylenethickness = 0.003
+    hdpethickness = 0.003
     skidthickness = 0.006
     bowtieheight = 0.025
-    
+
     # Set origin for rotation to geometric centre of antenna in x-y plane if required
     if rotate90:
         rotate90origin = (x, y)
@@ -204,7 +205,7 @@ def antenna_like_MALA_1200(x, y, z, resolution=0.001, rotate90=False, **kwargs):
     else:
         rotate90origin = ()
         output = 'Ey'
-    
+
     # Unknown properties
     if kwargs:
         excitationfreq = kwargs['excitationfreq']
@@ -217,13 +218,13 @@ def antenna_like_MALA_1200(x, y, z, resolution=0.001, rotate90=False, **kwargs):
         sourceresistance = 1000
         absorberEr = 6.49
         absorbersig = 0.252
-    
+
     x = x - (casesize[0] / 2)
     y = y - (casesize[1] / 2)
-    
+
     # Coordinates of source excitation point in antenna
     tx = x + 0.063, y + 0.052, z + skidthickness
-    
+
     if resolution == 0.001:
         dx = 0.001
         dy = 0.001
@@ -234,25 +235,25 @@ def antenna_like_MALA_1200(x, y, z, resolution=0.001, rotate90=False, **kwargs):
         dz = 0.002
         cavitysize = (0.062, 0.062, 0.036)
         cavitythickness = 0.002
-        polypropylenethickness = 0.002;
-        hdpethickness = 0.004;
+        polypropylenethickness = 0.002
+        hdpethickness = 0.004
         bowtieheight = 0.024
         tx = x + 0.062, y + 0.052, z + skidthickness
     else:
         raise CmdInputError('This antenna module can only be used with a spatial resolution of 1mm or 2mm')
-    
+
     # SMD resistors - 3 on each Tx & Rx bowtie arm
-    txres = 470 # Ohms
-    txrescellupper = txres / 3 # Resistor over 3 cells
-    txsigupper = ((1 / txrescellupper) * (dy / (dx * dz))) / 2 # Divide by number of parallel edges per resistor
-    txrescelllower = txres / 4 # Resistor over 4 cells
-    txsiglower = ((1 / txrescelllower) * (dy / (dx * dz))) / 2 # Divide by number of parallel edges per resistor
-    rxres = 150 # Ohms
-    rxrescellupper = rxres / 3 # Resistor over 3 cells
-    rxsigupper = ((1 / rxrescellupper) * (dy / (dx * dz))) / 2 # Divide by number of parallel edges per resistor
-    rxrescelllower = rxres / 4 # Resistor over 4 cells
-    rxsiglower = ((1 / rxrescelllower) * (dy / (dx * dz))) / 2 # Divide by number of parallel edges per resistor
-    
+    txres = 470  # Ohms
+    txrescellupper = txres / 3  # Resistor over 3 cells
+    txsigupper = ((1 / txrescellupper) * (dy / (dx * dz))) / 2  # Divide by number of parallel edges per resistor
+    txrescelllower = txres / 4  # Resistor over 4 cells
+    txsiglower = ((1 / txrescelllower) * (dy / (dx * dz))) / 2  # Divide by number of parallel edges per resistor
+    rxres = 150  # Ohms
+    rxrescellupper = rxres / 3  # Resistor over 3 cells
+    rxsigupper = ((1 / rxrescellupper) * (dy / (dx * dz))) / 2  # Divide by number of parallel edges per resistor
+    rxrescelllower = rxres / 4  # Resistor over 4 cells
+    rxsiglower = ((1 / rxrescelllower) * (dy / (dx * dz))) / 2  # Divide by number of parallel edges per resistor
+
     # Material definitions
     material(absorberEr, absorbersig, 1, 0, 'absorber')
     material(3, 0, 1, 0, 'pcb')
@@ -262,17 +263,17 @@ def antenna_like_MALA_1200(x, y, z, resolution=0.001, rotate90=False, **kwargs):
     material(3, txsigupper, 1, 0, 'txresupper')
     material(3, rxsiglower, 1, 0, 'rxreslower')
     material(3, rxsigupper, 1, 0, 'rxresupper')
-    
+
     # Antenna geometry
     # Shield - metallic enclosure
     box(x, y, z + skidthickness, x + casesize[0], y + casesize[1], z + skidthickness + casesize[2], 'pec', rotate90origin=rotate90origin)
     box(x + 0.020, y + casethickness, z + skidthickness, x + 0.100, y + casesize[1] - casethickness, z + skidthickness + casethickness, 'free_space', rotate90origin=rotate90origin)
     box(x + 0.100, y + casethickness, z + skidthickness, x + casesize[0] - casethickness, y + casesize[1] - casethickness, z + skidthickness + casethickness, 'free_space', rotate90origin=rotate90origin)
-    
+
     # Absorber material
     box(x + 0.020, y + casethickness, z + skidthickness, x + 0.100, y + casesize[1] - casethickness, z + skidthickness + casesize[2] - casethickness, 'absorber', rotate90origin=rotate90origin)
     box(x + 0.100, y + casethickness, z + skidthickness, x + casesize[0] - casethickness, y + casesize[1] - casethickness, z + skidthickness + casesize[2] - casethickness, 'absorber', rotate90origin=rotate90origin)
-    
+
     # Shield - cylindrical sections
     cylinder(x + 0.055, y + casesize[1] - 0.008, z + skidthickness, x + 0.055, y + casesize[1] - 0.008, z + skidthickness + casesize[2] - casethickness, 0.008, 'pec', rotate90origin=rotate90origin)
     cylinder(x + 0.055, y + 0.008, z + skidthickness, x + 0.055, y + 0.008, z + skidthickness + casesize[2] - casethickness, 0.008, 'pec', rotate90origin=rotate90origin)
@@ -286,24 +287,24 @@ def antenna_like_MALA_1200(x, y, z, resolution=0.001, rotate90=False, **kwargs):
     box(x + 0.054, y + 0.014, z + skidthickness, x + 0.056, y + 0.016, z + skidthickness + casesize[2] - casethickness, 'free_space', rotate90origin=rotate90origin)
     box(x + 0.146, y + casesize[1] - 0.016, z + skidthickness, x + 0.148, y + casesize[1] - 0.014, z + skidthickness + casesize[2] - casethickness, 'free_space', rotate90origin=rotate90origin)
     box(x + 0.146, y + 0.014, z + skidthickness, x + 0.148, y + 0.016, z + skidthickness + casesize[2] - casethickness, 'free_space', rotate90origin=rotate90origin)
-    
+
     # PCB
     box(x + 0.020, y + 0.018, z + skidthickness, x + casesize[0] - casethickness, y + casesize[1] - 0.018, z + skidthickness + pcbthickness, 'pcb', rotate90origin=rotate90origin)
-    
+
     # Shield - Tx & Rx cavities
     box(x + 0.032, y + 0.022, z + skidthickness, x + 0.032 + cavitysize[0], y + 0.022 + cavitysize[1], z + skidthickness + cavitysize[2], 'pec', rotate90origin=rotate90origin)
     box(x + 0.032 + cavitythickness, y + 0.022 + cavitythickness, z + skidthickness, x + 0.032 + cavitysize[0] - cavitythickness, y + 0.022 + cavitysize[1] - cavitythickness, z + skidthickness + cavitysize[2], 'absorber', rotate90origin=rotate90origin)
     box(x + 0.108, y + 0.022, z + skidthickness, x + 0.108 + cavitysize[0], y + 0.022 + cavitysize[1], z + skidthickness + cavitysize[2], 'pec', rotate90origin=rotate90origin)
     box(x + 0.108 + cavitythickness, y + 0.022 + cavitythickness, z + skidthickness, x + 0.108 + cavitysize[0] - cavitythickness, y + 0.022 + cavitysize[1] - cavitythickness, z + skidthickness + cavitysize[2], 'free_space', rotate90origin=rotate90origin)
-    
+
     # Shield - Tx & Rx cavities - joining strips
     box(x + 0.032 + cavitysize[0], y + 0.022 + cavitysize[1] - 0.006, z + skidthickness + cavitysize[2] - casethickness, x + 0.108, y + 0.022 + cavitysize[1], z + skidthickness + cavitysize[2], 'pec', rotate90origin=rotate90origin)
     box(x + 0.032 + cavitysize[0], y + 0.022, z + skidthickness + cavitysize[2] - casethickness, x + 0.108, y + 0.022 + 0.006, z + skidthickness + cavitysize[2], 'pec', rotate90origin=rotate90origin)
-    
+
     # PCB - replace bits chopped by TX & Rx cavities
     box(x + 0.032 + cavitythickness, y + 0.022 + cavitythickness, z + skidthickness, x + 0.032 + cavitysize[0] - cavitythickness, y + 0.022 + cavitysize[1] - cavitythickness, z + skidthickness + pcbthickness, 'pcb', rotate90origin=rotate90origin)
     box(x + 0.108 + cavitythickness, y + 0.022 + cavitythickness, z + skidthickness, x + 0.108 + cavitysize[0] - cavitythickness, y + 0.022 + cavitysize[1] - cavitythickness, z + skidthickness + pcbthickness, 'pcb', rotate90origin=rotate90origin)
-    
+
     # PCB components
     # Tx bowtie
     if resolution == 0.001:
@@ -314,7 +315,7 @@ def antenna_like_MALA_1200(x, y, z, resolution=0.001, rotate90=False, **kwargs):
     elif resolution == 0.002:
         triangle(tx[0], tx[1], tx[2], tx[0] - 0.026, tx[1] - bowtieheight, tx[2], tx[0] + 0.026, tx[1] - bowtieheight, tx[2], 0, 'pec', rotate90origin=rotate90origin)
         triangle(tx[0], tx[1] + 0.002, tx[2], tx[0] - 0.026, tx[1] + bowtieheight + 0.002, tx[2], tx[0] + 0.026, tx[1] + bowtieheight + 0.002, tx[2], 0, 'pec', rotate90origin=rotate90origin)
-    
+
     # Rx bowtie
     if resolution == 0.001:
         triangle(tx[0] + 0.076, tx[1] - 0.001, tx[2], tx[0] + 0.076 - 0.026, tx[1] - bowtieheight - 0.001, tx[2], tx[0] + 0.076 + 0.026, tx[1] - bowtieheight - 0.001, tx[2], 0, 'pec', rotate90origin=rotate90origin)
@@ -324,7 +325,7 @@ def antenna_like_MALA_1200(x, y, z, resolution=0.001, rotate90=False, **kwargs):
     elif resolution == 0.002:
         triangle(tx[0] + 0.076, tx[1], tx[2], tx[0] + 0.076 - 0.026, tx[1] - bowtieheight, tx[2], tx[0] + 0.076 + 0.026, tx[1] - bowtieheight, tx[2], 0, 'pec', rotate90origin=rotate90origin)
         triangle(tx[0] + 0.076, tx[1] + 0.002, tx[2], tx[0] + 0.076 - 0.026, tx[1] + bowtieheight + 0.002, tx[2], tx[0] + 0.076 + 0.026, tx[1] + bowtieheight + 0.002, tx[2], 0, 'pec', rotate90origin=rotate90origin)
-    
+
     # Tx surface mount resistors (lower y coordinate)
     if resolution == 0.001:
         edge(tx[0] - 0.023, tx[1] - bowtieheight - 0.004, tx[2], tx[0] - 0.023, tx[1] - bowtieheight - dy, tx[2], 'txreslower', rotate90origin=rotate90origin)
@@ -340,7 +341,7 @@ def antenna_like_MALA_1200(x, y, z, resolution=0.001, rotate90=False, **kwargs):
         edge(tx[0] + dx, tx[1] - bowtieheight - 0.004, tx[2], tx[0] + dx, tx[1] - bowtieheight, tx[2], 'txreslower', rotate90origin=rotate90origin)
         edge(tx[0] + 0.020, tx[1] - bowtieheight - 0.004, tx[2], tx[0] + 0.020, tx[1] - bowtieheight, tx[2], 'txreslower', rotate90origin=rotate90origin)
         edge(tx[0] + 0.020 + dx, tx[1] - bowtieheight - 0.004, tx[2], tx[0] + 0.020 + dx, tx[1] - bowtieheight, tx[2], 'txreslower', rotate90origin=rotate90origin)
-    
+
     # Tx surface mount resistors (upper y coordinate)
     if resolution == 0.001:
         edge(tx[0] - 0.023, tx[1] + bowtieheight + 0.002, tx[2], tx[0] - 0.023, tx[1] + bowtieheight + 0.006, tx[2], 'txresupper', rotate90origin=rotate90origin)
@@ -356,7 +357,7 @@ def antenna_like_MALA_1200(x, y, z, resolution=0.001, rotate90=False, **kwargs):
         edge(tx[0] + dx, tx[1] + bowtieheight + 0.002, tx[2], tx[0] + dx, tx[1] + bowtieheight + 0.006, tx[2], 'txresupper', rotate90origin=rotate90origin)
         edge(tx[0] + 0.020, tx[1] + bowtieheight + 0.002, tx[2], tx[0] + 0.020, tx[1] + bowtieheight + 0.006, tx[2], 'txresupper', rotate90origin=rotate90origin)
         edge(tx[0] + 0.020 + dx, tx[1] + bowtieheight + 0.002, tx[2], tx[0] + 0.020 + dx, tx[1] + bowtieheight + 0.006, tx[2], 'txresupper', rotate90origin=rotate90origin)
-    
+
     # Rx surface mount resistors (lower y coordinate)
     if resolution == 0.001:
         edge(tx[0] - 0.023 + 0.076, tx[1] - bowtieheight - 0.004, tx[2], tx[0] - 0.023 + 0.076, tx[1] - bowtieheight - dy, tx[2], 'rxreslower', rotate90origin=rotate90origin)
@@ -372,7 +373,7 @@ def antenna_like_MALA_1200(x, y, z, resolution=0.001, rotate90=False, **kwargs):
         edge(tx[0] + dx + 0.076, tx[1] - bowtieheight - 0.004, tx[2], tx[0] + dx + 0.076, tx[1] - bowtieheight, tx[2], 'rxreslower', rotate90origin=rotate90origin)
         edge(tx[0] + 0.020 + 0.076, tx[1] - bowtieheight - 0.004, tx[2], tx[0] + 0.020 + 0.076, tx[1] - bowtieheight, tx[2], 'rxreslower', rotate90origin=rotate90origin)
         edge(tx[0] + 0.020 + dx + 0.076, tx[1] - bowtieheight - 0.004, tx[2], tx[0] + 0.020 + dx + 0.076, tx[1] - bowtieheight, tx[2], 'rxreslower', rotate90origin=rotate90origin)
-    
+
     # Rx surface mount resistors (upper y coordinate)
     if resolution == 0.001:
         edge(tx[0] - 0.023 + 0.076, tx[1] + bowtieheight + 0.002, tx[2], tx[0] - 0.023 + 0.076, tx[1] + bowtieheight + 0.006, tx[2], 'rxresupper', rotate90origin=rotate90origin)
@@ -388,7 +389,7 @@ def antenna_like_MALA_1200(x, y, z, resolution=0.001, rotate90=False, **kwargs):
         edge(tx[0] + dx + 0.076, tx[1] + bowtieheight + 0.002, tx[2], tx[0] + dx + 0.076, tx[1] + bowtieheight + 0.006, tx[2], 'rxresupper', rotate90origin=rotate90origin)
         edge(tx[0] + 0.020 + 0.076, tx[1] + bowtieheight + 0.002, tx[2], tx[0] + 0.020 + 0.076, tx[1] + bowtieheight + 0.006, tx[2], 'rxresupper', rotate90origin=rotate90origin)
         edge(tx[0] + 0.020 + dx + 0.076, tx[1] + bowtieheight + 0.002, tx[2], tx[0] + 0.020 + dx + 0.076, tx[1] + bowtieheight + 0.006, tx[2], 'rxresupper', rotate90origin=rotate90origin)
-    
+
     # Skid
     box(x, y, z, x + casesize[0], y + casesize[1], z + polypropylenethickness, 'polypropylene', rotate90origin=rotate90origin)
     box(x, y, z + polypropylenethickness, x + casesize[0], y + casesize[1], z + polypropylenethickness + hdpethickness, 'hdpe', rotate90origin=rotate90origin)
@@ -396,11 +397,10 @@ def antenna_like_MALA_1200(x, y, z, resolution=0.001, rotate90=False, **kwargs):
     # Geometry views
     #geometry_view(x - dx, y - dy, z - dz, x + casesize[0] + dx, y + casesize[1] + dy, z + casesize[2] + skidthickness + dz, dx, dy, dz, 'antenna_like_MALA_1200')
     #geometry_view(x, y, z, x + casesize[0], y + casesize[1], z + 0.010, dx, dy, dz, 'antenna_like_MALA_1200_pcb', type='f')
-    
+
     # Excitation
     print('#waveform: gaussian 1.0 {} myGaussian'.format(excitationfreq))
     voltage_source('y', tx[0], tx[1], tx[2], sourceresistance, 'myGaussian', dxdy=(resolution, resolution), rotate90origin=rotate90origin)
-    
+
     # Output point - receiver bowtie
     rx(tx[0] + 0.076, tx[1], tx[2], identifier='rxbowtie', to_save=[output], polarisation='y', dxdy=(resolution, resolution), rotate90origin=rotate90origin)
-

user_libs/optimisation_taguchi/fitness_functions.py

@@ -24,6 +24,7 @@ from gprMax.exceptions import GeneralError
     The second argument is a dictionary which can contain any number of additional arguments, e.g. names (IDs) of outputs (rxs) from input file
 """
 
+
 def min_max_value(filename, args):
     """Minimum value from a response.
 
@@ -78,8 +79,8 @@ def xcorr(filename, args):
         raise GeneralError('Cannot load reference response from {}'.format(refrespfile))
     with open(refrespfile, 'r') as f:
         refdata = np.loadtxt(f)
-    reftime = refdata[:,0] * 1e-9
-    refresp = refdata[:,1]
+    reftime = refdata[:, 0] * 1e-9
+    refresp = refdata[:, 1]
 
     # Load response from output file
     f = h5py.File(filename, 'r')
@@ -131,8 +132,8 @@ def xcorr(filename, args):
     #fig, ax = plt.subplots(subplot_kw=dict(xlabel='Iterations', ylabel='Voltage [V]'), figsize=(20, 10), facecolor='w', edgecolor='w')
     #ax.plot(refresp,'r', lw=2, label='refresp')
     #ax.plot(modelresp,'b', lw=2, label='modelresp')
-    #ax.grid()
-    #plt.show()
+    # ax.grid()
+    # plt.show()
 
     # Calculate cross-correlation
     xcorr = signal.correlate(refresp, modelresp)
@@ -224,7 +225,7 @@ def compactness(filename, args):
             peak = np.amax([np.amax(outputdata), np.abs(np.amin(outputdata))])
 
             # Get peaks and troughs in signal
-            delta = peak / 50 # Considered a peak/trough if it has the max/min value, and was preceded (to the left) by a value lower by delta
+            delta = peak / 50  # Considered a peak/trough if it has the max/min value, and was preceded (to the left) by a value lower by delta
             maxtab, mintab = peakdet(outputdata, delta)
             peaks = maxtab + mintab
             peaks.sort()
@@ -271,8 +272,8 @@ def spectral_centroid(x, samplerate):
     magnitudes = np.abs(np.fft.rfft(x))
     length = len(x)
     # Positive frequencies
-    freqs = np.abs(np.fft.fftfreq(length, 1.0/samplerate)[:length//2+1])
-    centroid = np.sum(magnitudes*freqs) / np.sum(magnitudes)
+    freqs = np.abs(np.fft.fftfreq(length, 1.0 / samplerate)[:length // 2 + 1])
+    centroid = np.sum(magnitudes * freqs) / np.sum(magnitudes)
 
     return centroid
 
@@ -294,7 +295,7 @@ def zero_crossings(x):
     return indexzeros
 
 
-def peakdet(v, delta, x = None):
+def peakdet(v, delta, x=None):
     """Detect peaks and troughs in a vector (adapted from MATLAB script at http://billauer.co.il/peakdet.html).
         A point is considered a maximum peak if it has the maximal value, and was preceded (to the left) by a value lower by delta.
 
@@ -341,14 +342,14 @@ def peakdet(v, delta, x = None):
             mnpos = x[i]
 
         if lookformax:
-            if this < mx-delta:
+            if this < mx - delta:
                 if int(mxpos) != 0:
                     maxtab.append(int(mxpos))
                     mn = this
                     mnpos = x[i]
                     lookformax = False
         else:
-            if this > mn+delta:
+            if this > mn + delta:
                 if int(mnpos) != 0:
                     mintab.append(int(mnpos))
                     mx = this

user_libs/optimisation_taguchi/plot_results.py

@@ -32,7 +32,7 @@ for item in optparamsinit:
 print('History of parameter values:')
 for key, value in optparamshist.items():
     print('\t{}: {}'.format(key, value))
-      
-    
+
+
 # Plot the history of fitness values and each optimised parameter values for the optimisation
 plot_optimisation_history(fitnessvalueshist, optparamshist, optparamsinit)