Re-structuring package layout

testing/test_experimental.py

@@ -0,0 +1,103 @@
+# Copyright (C) 2015-2022: The University of Edinburgh, United Kingdom
+#                 Authors: Craig Warren, Antonis Giannopoulos, and John Hartley
+#
+# This file is part of gprMax.
+#
+# gprMax is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# gprMax is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with gprMax.  If not, see <http://www.gnu.org/licenses/>.
+
+import argparse
+import logging
+from pathlib import Path
+
+import h5py
+import matplotlib.pyplot as plt
+import numpy as np
+
+logger = logging.getLogger(__name__)
+
+"""Plots a comparison of fields between given simulation output and experimental 
+    data files.
+"""
+
+# Parse command line arguments
+parser = argparse.ArgumentParser(description='Plots a comparison of fields between ' +
+                                    'given simulation output and experimental data files.', 
+                                 usage='cd gprMax; python -m tests.test_experimental modelfile realfile output')
+parser.add_argument('modelfile', help='name of model output file including path')
+parser.add_argument('realfile', help='name of file containing experimental data including path')
+parser.add_argument('output', help='output to be plotted, i.e. Ex Ey Ez', nargs='+')
+args = parser.parse_args()
+
+modelfile = Path(args.modelfile)
+realfile = Path(args.realfile)
+
+# Model results
+f = h5py.File(Path(modelfile), 'r')
+path = '/rxs/rx1/'
+availablecomponents = list(f[path].keys())
+
+# Check for polarity of output and if requested output is in file
+if args.output[0][0] == 'm':
+    polarity = -1
+    args.outputs[0] = args.output[0][1:]
+else:
+    polarity = 1
+
+if args.output[0] not in availablecomponents:
+    logger.exception(f"{args.output[0]} output requested to plot, but the " +
+                     f"available output for receiver 1 is {', '.join(availablecomponents)}")
+    raise ValueError
+
+floattype = f[path + args.output[0]].dtype
+iterations = f.attrs['Iterations']
+dt = f.attrs['dt']
+model = np.zeros(iterations, dtype=floattype)
+model = f[path + args.output[0]][:] * polarity
+model /= np.amax(np.abs(model))
+timemodel = np.linspace(0, 1, iterations)
+timemodel *= (iterations * dt)
+f.close()
+
+# Find location of maximum value from model
+modelmax = np.where(np.abs(model) == 1)[0][0]
+
+# Real results
+with open(realfile, 'r') as f:
+    real = np.loadtxt(f)
+real[:, 1] = real[:, 1] / np.amax(np.abs(real[:, 1]))
+realmax = np.where(np.abs(real[:, 1]) == 1)[0][0]
+
+difftime = - (timemodel[modelmax] - real[realmax, 0])
+
+# Plot modelled and real data
+fig, ax = plt.subplots(num=modelfile.stem + '_vs_' + realfile.stem, 
+                       figsize=(20, 10), facecolor='w', edgecolor='w')
+ax.plot(timemodel + difftime, model, 'r', lw=2, label='Model')
+ax.plot(real[:, 0], real[:, 1], 'r', ls='--', lw=2, label='Experiment')
+ax.set_xlabel('Time [s]')
+ax.set_ylabel('Amplitude')
+ax.set_xlim([0, timemodel[-1]])
+# ax.set_ylim([-1, 1])
+ax.legend()
+ax.grid()
+
+# Save a PDF/PNG of the figure
+savename =  modelfile.stem + '_vs_' + realfile.stem
+savename = modelfile.parent / savename
+# fig.savefig(savename.with_suffix('.pdf'), dpi=None, format='pdf', 
+#             bbox_inches='tight', pad_inches=0.1)
+# fig.savefig(savename.with_suffix('.png'), dpi=150, format='png', 
+#             bbox_inches='tight', pad_inches=0.1)
+
+plt.show()