Refactor existing model tests to use pytest

requirements.txt

@@ -19,4 +19,9 @@ numpy-stl
 terminaltables
 tqdm
 wheel
+pytest
+pytest-benchmark
+pytest-benchmark[histogram]
+pytest-mpi
+pytest-regressions
 git+https://github.com/craig-warren/PyEVTK.git

tests/data/models_analytical/hertzian_dipole_fs_analytical.in

@@ -0,0 +1,8 @@
+#title: Hertzian dipole in free-space
+#domain: 0.100 0.100 0.100
+#dx_dy_dz: 0.001 0.001 0.001
+#time_window: 3e-9
+
+#waveform: gaussianprime 1 1e9 myWave
+#hertzian_dipole: z 0.050 0.050 0.050 myWave
+#rx: 0.070 0.070 0.070

tests/data/models_basic/2D_ExHyHz/2D_ExHyHz.in

@@ -0,0 +1,8 @@
+#title: 2D test Ex, Hy, Hz components
+#domain: 0.001 0.100 0.100
+#dx_dy_dz: 0.001 0.001 0.001
+#time_window: 3e-9
+
+#waveform: gaussiandot 1 1e9 myWave
+#hertzian_dipole: x 0 0.050 0.050 myWave
+#rx: 0 0.070 0.070

tests/data/models_basic/2D_EyHxHz/2D_EyHxHz.in

@@ -0,0 +1,8 @@
+#title: 2D test Ey, Hx, Hz components
+#domain: 0.100 0.001 0.100
+#dx_dy_dz: 0.001 0.001 0.001
+#time_window: 3e-9
+
+#waveform: gaussiandot 1 1e9 myWave
+#hertzian_dipole: y 0.050 0 0.050 myWave
+#rx: 0.070 0 0.070

tests/data/models_basic/2D_EzHxHy/2D_EzHxHy.in

@@ -0,0 +1,8 @@
+#title: 2D test Ez, Hx, Hy components
+#domain: 0.100 0.100 0.001
+#dx_dy_dz: 0.001 0.001 0.001
+#time_window: 3e-9
+
+#waveform: gaussiandot 1 1e9 myWave
+#hertzian_dipole: z 0.050 0.050 0 myWave
+#rx: 0.070 0.070 0

tests/data/models_basic/cylinder_Ascan_2D/cylinder_Ascan_2D.in

@@ -0,0 +1,13 @@
+#title: A-scan from a metal cylinder buried in a dielectric half-space
+#domain: 0.240 0.210 0.002
+#dx_dy_dz: 0.002 0.002 0.002
+#time_window: 3e-9
+
+#material: 6 0 1 0 half_space
+
+#waveform: ricker 1 1.5e9 my_ricker
+#hertzian_dipole: z 0.100 0.170 0 my_ricker
+#rx: 0.140 0.170 0
+
+#box: 0 0 0 0.240 0.170 0.002 half_space
+#cylinder: 0.120 0.080 0 0.120 0.080 0.002 0.010 pec

tests/data/models_basic/hertzian_dipole_dispersive/hertzian_dipole_dispersive.in

@@ -0,0 +1,12 @@
+#title: Hertzian dipole in water
+#domain: 0.100 0.100 0.100
+#dx_dy_dz: 0.001 0.001 0.001
+#time_window: 3e-9
+
+#waveform: gaussiandot 1 1e9 myWave
+#hertzian_dipole: z 0.050 0.050 0.050 myWave
+#rx: 0.070 0.070 0.070
+
+#material: 4.9 0 1 0 myWater
+#add_dispersion_debye: 1 75.2 9.231e-12 myWater
+#box: 0 0 0 0.100 0.100 0.100 myWater

tests/data/models_basic/hertzian_dipole_fs/hertzian_dipole_fs.in

@@ -0,0 +1,8 @@
+#title: Hertzian dipole in free-space
+#domain: 0.100 0.100 0.100
+#dx_dy_dz: 0.001 0.001 0.001
+#time_window: 3e-9
+
+#waveform: gaussiandot 1 1e9 myWave
+#hertzian_dipole: z 0.050 0.050 0.050 myWave
+#rx: 0.070 0.070 0.070

tests/data/models_basic/hertzian_dipole_hs/hertzian_dipole_hs.in

@@ -0,0 +1,11 @@
+#title: Hertzian dipole over a half-space
+#domain: 0.100 0.100 0.100
+#dx_dy_dz: 0.001 0.001 0.001
+#time_window: 3e-9
+
+#waveform: gaussiandot 1 1e9 myWave
+#hertzian_dipole: z 0.050 0.050 0.050 myWave
+#rx: 0.070 0.070 0.070
+
+#material: 8 0 1 0 half_space
+#box: 0 0 0 0.100 0.100 0.050 half_space

tests/data/models_basic/magnetic_dipole_fs/magnetic_dipole_fs.in

@@ -0,0 +1,8 @@
+#title: Magnetic dipole in free-space
+#domain: 0.100 0.100 0.100
+#dx_dy_dz: 0.001 0.001 0.001
+#time_window: 3e-9
+
+#waveform: gaussiandot 1 1e9 myWave
+#magnetic_dipole: z 0.050 0.050 0.050 myWave
+#rx: 0.070 0.070 0.070

tests/test_models.py

@@ -0,0 +1,135 @@
+# Copyright (C) 2015-2023: 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 logging
+import sys
+from pathlib import Path
+
+import h5py
+import matplotlib.pyplot as plt
+import numpy as np
+import pytest
+
+import gprMax
+from testing.analytical_solutions import hertzian_dipole_fs
+from tests.utilities.data import get_data_from_h5_file, calculate_diffs
+from tests.utilities.plotting import plot_dataset_comparison, plot_diffs
+
+from gprMax.utilities.logging import logging_config
+
+logger = logging.getLogger(__name__)
+logging_config(name=__name__)
+
+if sys.platform == "linux":
+    plt.switch_backend("agg")
+
+
+"""Compare field outputs
+
+    Usage:
+        cd gprMax
+        pytest tests/test_models.py
+"""
+
+# Specify directory containing basic models to test
+BASIC_MODELS_DIRECTORY = Path(__file__).parent / "data" / "models_basic"
+
+# List of available basic test models
+BASIC_MODELS = [
+    "2D_ExHyHz",
+    "2D_EyHxHz",
+    "2D_EzHxHy",
+    "cylinder_Ascan_2D",
+    "hertzian_dipole_fs",
+    "hertzian_dipole_hs",
+    "hertzian_dipole_dispersive",
+    "magnetic_dipole_fs",
+]
+
+# Specify directory containing analytical models to test
+ANALYTICAL_MODELS_DIRECTORY = Path(__file__).parent / "data" / "models_analytical"
+
+# List of available analytical models
+ANALYTICAL_MODELS = ["hertzian_dipole_fs_analytical"]
+
+FIELD_COMPONENTS_BASE_PATH = "/rxs/rx1/"
+
+
+def run_test(model_name, input_base, data_directory, analytical_func=None, gpu=None, opencl=None):
+    input_filepath = input_base.with_suffix(".in")
+    reference_filepath = Path(f"{input_base}_ref.h5")
+    
+    output_base = data_directory / model_name
+    output_filepath = output_base.with_suffix(".h5")
+
+    # Run model
+    gprMax.run(inputfile=input_filepath, outputfile=output_filepath, gpu=gpu, opencl=opencl)
+
+    test_time, test_data = get_data_from_h5_file(output_filepath)
+
+    if analytical_func is not None:
+        ref_time = test_time
+        ref_data = analytical_func(output_filepath)
+    else:
+        ref_time, ref_data = get_data_from_h5_file(reference_filepath)
+
+    fig1 = plot_dataset_comparison(test_time, test_data, ref_time, ref_data, model_name)
+    fig1.savefig(output_base.with_suffix(".png"), dpi=150, format="png", bbox_inches="tight", pad_inches=0.1)
+
+    # Required to correctly calculate diffs
+    assert test_time.shape == ref_time.shape
+    assert np.all(test_time == ref_time)
+    assert test_data.shape == ref_data.shape
+
+    data_diffs = calculate_diffs(test_data, ref_data)
+    max_diff = round(np.max(data_diffs), 2)
+
+    fig2 = plot_diffs(test_time, data_diffs)
+    fig2.savefig(Path(f"{output_base}_diffs.png"), dpi=150, format="png", bbox_inches="tight", pad_inches=0.1)
+
+    logger.info(f"Output data folder: {data_directory}")
+
+    assert max_diff <= 0
+
+
+def calc_hertzian_dipole_fs_analytical_solution(filepath):
+    with h5py.File(filepath, "r") as file:
+        # Tx/Rx position to feed to analytical solution
+        rx_pos = file[FIELD_COMPONENTS_BASE_PATH].attrs["Position"]
+        tx_pos = file["/srcs/src1/"].attrs["Position"]
+        rx_pos_relative = ((rx_pos[0] - tx_pos[0]), (rx_pos[1] - tx_pos[1]), (rx_pos[2] - tx_pos[2]))
+
+        # Analytical solution of a dipole in free space
+        data = hertzian_dipole_fs(
+            file.attrs["Iterations"], file.attrs["dt"], file.attrs["dx_dy_dz"], rx_pos_relative
+        )
+    return data
+
+
+@pytest.mark.parametrize("model", BASIC_MODELS)
+def test_basic_models(model, datadir):
+
+    base_filepath = Path(BASIC_MODELS_DIRECTORY, model, model)
+    run_test(model, base_filepath, datadir)
+
+
+@pytest.mark.parametrize("model", ANALYTICAL_MODELS)
+def test_analyitical_models(model, datadir):
+
+    base_filepath = Path(ANALYTICAL_MODELS_DIRECTORY, model)
+    run_test(model, base_filepath, datadir, analytical_func=calc_hertzian_dipole_fs_analytical_solution)

tests/utilities/data.py

@@ -0,0 +1,53 @@
+import logging
+
+import h5py
+import numpy as np
+
+from gprMax.utilities.logging import logging_config
+
+logger = logging.getLogger(__name__)
+logging_config(name=__name__)
+
+
+FIELD_COMPONENTS_BASE_PATH = "/rxs/rx1/"
+
+
+def get_data_from_h5_file(h5_filepath):
+    with h5py.File(h5_filepath, "r") as h5_file:
+        # Get available field output component names and datatype
+        field_components = list(h5_file[FIELD_COMPONENTS_BASE_PATH].keys())
+        dtype = h5_file[FIELD_COMPONENTS_BASE_PATH + field_components[0]].dtype
+        shape = h5_file[FIELD_COMPONENTS_BASE_PATH + str(field_components[0])].shape
+
+        # Arrays for storing field data
+        if len(shape) == 1:
+            data = np.zeros((h5_file.attrs["Iterations"], len(field_components)), dtype=dtype)
+        else:  # Merged B-scan data
+            data = np.zeros((h5_file.attrs["Iterations"], len(field_components), shape[1]), dtype=dtype)
+        for index, field_component in enumerate(field_components):
+            data[:, index] = h5_file[FIELD_COMPONENTS_BASE_PATH + str(field_component)]
+            if np.any(np.isnan(data[:, index])):
+                logger.exception("Data contains NaNs")
+                raise ValueError
+
+        max_time = (h5_file.attrs["Iterations"] - 1) * h5_file.attrs["dt"] / 1e-9
+        time = np.linspace(0, max_time, num=h5_file.attrs["Iterations"])
+
+    return time, data
+
+
+def calculate_diffs(test_data, ref_data):
+    diffs = np.zeros(test_data.shape, dtype=np.float64)
+    for i in range(test_data.shape[1]):
+        maxi = np.amax(np.abs(ref_data[:, i]))
+        diffs[:, i] = np.divide(
+            np.abs(ref_data[:, i] - test_data[:, i]), maxi, out=np.zeros_like(ref_data[:, i]), where=maxi != 0
+        )  # Replace any division by zero with zero
+
+        # Calculate power (ignore warning from taking a log of any zero values)
+        with np.errstate(divide="ignore"):
+            diffs[:, i] = 20 * np.log10(diffs[:, i])
+        # Replace any NaNs or Infs from zero division
+        diffs[:, i][np.invert(np.isfinite(diffs[:, i]))] = 0
+
+    return diffs

tests/utilities/plotting.py

@@ -0,0 +1,85 @@
+from matplotlib import pyplot as plt
+import numpy as np
+
+
+def _plot_data(subplots, time, data, label=None, colour="r", line_style="-"):
+    for i in range(data.shape[1]):
+        subplots[i].plot(time, data[:, i], colour, lw=2, ls=line_style, label=label)
+
+
+def plot_dataset_comparison(test_time, test_data, ref_time, ref_data, model_name):
+    fig, ((ex, hx), (ey, hy), (ez, hz)) = plt.subplots(
+        nrows=3,
+        ncols=2,
+        sharex=False,
+        sharey="col",
+        subplot_kw=dict(xlabel="Time [ns]"),
+        figsize=(20, 10),
+        facecolor="w",
+        edgecolor="w",
+    )
+
+    subplots = [ex, ey, ez, hx, hy, hz]
+    _plot_data(subplots, test_time, test_data, model_name)
+    _plot_data(subplots, ref_time, ref_data, f"{model_name} (Ref)", "g", "--")
+
+    ylabels = [
+        "$E_x$, field strength [V/m]",
+        "$H_x$, field strength [A/m]",
+        "$E_y$, field strength [V/m]",
+        "$H_y$, field strength [A/m]",
+        "$E_z$, field strength [V/m]",
+        "$H_z$, field strength [A/m]",
+    ]
+
+    x_max = max(np.max(test_time), np.max(ref_time))
+    for i, ax in enumerate(fig.axes):
+        ax.set_ylabel(ylabels[i])
+        ax.set_xlim(0, x_max)
+        ax.grid()
+        ax.legend()
+
+    return fig
+
+
+def plot_diffs(time, diffs, plot_min=-160):
+    """Plots ...
+
+    Args:
+        time: 
+        diffs: 
+        plot_min: minimum value of difference to plot (dB). Default: -160
+
+    Returns:
+        plt: matplotlib plot object.
+    """
+    fig, ((ex, hx), (ey, hy), (ez, hz)) = plt.subplots(
+        nrows=3,
+        ncols=2,
+        sharex=False,
+        sharey="col",
+        subplot_kw=dict(xlabel="Time [ns]"),
+        figsize=(20, 10),
+        facecolor="w",
+        edgecolor="w",
+    )
+    _plot_data([ex, ey, ez, hx, hy, hz], time, diffs)
+
+    ylabels = [
+        "$E_x$, difference [dB]",
+        "$H_x$, difference [dB]",
+        "$E_y$, difference [dB]",
+        "$H_y$, difference [dB]",
+        "$E_z$, difference [dB]",
+        "$H_z$, difference [dB]",
+    ]
+
+    x_max = np.max(time)
+    y_max = np.max(diffs)
+    for i, ax in enumerate(fig.axes):
+        ax.set_ylabel(ylabels[i])
+        ax.set_xlim(0, x_max)
+        ax.set_ylim(plot_min, y_max)
+        ax.grid()
+
+    return fig