diff --git a/user_models/antenna_like_GSSI_1500_fs.py b/examples/antenna_like_GSSI_1500_fs.py similarity index 99% rename from user_models/antenna_like_GSSI_1500_fs.py rename to examples/antenna_like_GSSI_1500_fs.py index e81108c3..817a00d3 100644 --- a/user_models/antenna_like_GSSI_1500_fs.py +++ b/examples/antenna_like_GSSI_1500_fs.py @@ -45,4 +45,4 @@ scene.add(gv1) scene.add(gv2) # Run model -gprMax.run(scenes=[scene], geometry_only=True, outputfile=fn, gpu=[0]) +gprMax.run(scenes=[scene], geometry_only=True, outputfile=fn, gpu=None) diff --git a/user_models/antenna_wire_dipole_fs.py b/examples/antenna_wire_dipole_fs.py similarity index 100% rename from user_models/antenna_wire_dipole_fs.py rename to examples/antenna_wire_dipole_fs.py diff --git a/examples/cylinder_Ascan_2D.h5 b/examples/cylinder_Ascan_2D.h5 new file mode 100644 index 00000000..2db08bb9 Binary files /dev/null and b/examples/cylinder_Ascan_2D.h5 differ diff --git a/user_models/cylinder_Ascan_2D.in b/examples/cylinder_Ascan_2D.in similarity index 100% rename from user_models/cylinder_Ascan_2D.in rename to examples/cylinder_Ascan_2D.in diff --git a/user_models/cylinder_Bscan_2D.in b/examples/cylinder_Bscan_2D.in similarity index 100% rename from user_models/cylinder_Bscan_2D.in rename to examples/cylinder_Bscan_2D.in diff --git a/examples/cylinder_half_space.vti b/examples/cylinder_half_space.vti new file mode 100644 index 00000000..31e29847 Binary files /dev/null and b/examples/cylinder_half_space.vti differ diff --git a/user_models/heterogeneous_soil.in b/examples/heterogeneous_soil.in similarity index 100% rename from user_models/heterogeneous_soil.in rename to examples/heterogeneous_soil.in diff --git a/tools/Jupyter_notebooks/README.rst b/examples/jupyter-notebooks/README.rst similarity index 100% rename from tools/Jupyter_notebooks/README.rst rename to examples/jupyter-notebooks/README.rst diff --git a/tools/Jupyter_notebooks/cylinder_half_space_geo.png b/examples/jupyter-notebooks/cylinder_half_space_geo.png similarity index 100% rename from tools/Jupyter_notebooks/cylinder_half_space_geo.png rename to examples/jupyter-notebooks/cylinder_half_space_geo.png diff --git a/tools/Jupyter_notebooks/example_Ascan_2D.ipynb b/examples/jupyter-notebooks/example_Ascan_2D.ipynb similarity index 100% rename from tools/Jupyter_notebooks/example_Ascan_2D.ipynb rename to examples/jupyter-notebooks/example_Ascan_2D.ipynb diff --git a/tools/Jupyter_notebooks/example_Bscan_2D.ipynb b/examples/jupyter-notebooks/example_Bscan_2D.ipynb similarity index 100% rename from tools/Jupyter_notebooks/example_Bscan_2D.ipynb rename to examples/jupyter-notebooks/example_Bscan_2D.ipynb diff --git a/tools/Jupyter_notebooks/plot_Ascan.ipynb b/examples/jupyter-notebooks/plot_Ascan.ipynb similarity index 100% rename from tools/Jupyter_notebooks/plot_Ascan.ipynb rename to examples/jupyter-notebooks/plot_Ascan.ipynb diff --git a/tools/Jupyter_notebooks/plot_Bscan.ipynb b/examples/jupyter-notebooks/plot_Bscan.ipynb similarity index 100% rename from tools/Jupyter_notebooks/plot_Bscan.ipynb rename to examples/jupyter-notebooks/plot_Bscan.ipynb diff --git a/tools/Jupyter_notebooks/plot_antenna_params.ipynb b/examples/jupyter-notebooks/plot_antenna_params.ipynb similarity index 100% rename from tools/Jupyter_notebooks/plot_antenna_params.ipynb rename to examples/jupyter-notebooks/plot_antenna_params.ipynb diff --git a/tools/Jupyter_notebooks/plot_source_wave.ipynb b/examples/jupyter-notebooks/plot_source_wave.ipynb similarity index 100% rename from tools/Jupyter_notebooks/plot_source_wave.ipynb rename to examples/jupyter-notebooks/plot_source_wave.ipynb diff --git a/user_models/sub-gridding/gssi_400_over_fractal_subsurface.py b/examples/sub-gridding/gssi_400_over_fractal_subsurface.py similarity index 100% rename from user_models/sub-gridding/gssi_400_over_fractal_subsurface.py rename to examples/sub-gridding/gssi_400_over_fractal_subsurface.py diff --git a/user_models/sub-gridding/subgrid_basic.py b/examples/sub-gridding/subgrid_basic.py similarity index 74% rename from user_models/sub-gridding/subgrid_basic.py rename to examples/sub-gridding/subgrid_basic.py index 8bc9eb41..196b39b3 100644 --- a/user_models/sub-gridding/subgrid_basic.py +++ b/examples/sub-gridding/subgrid_basic.py @@ -4,35 +4,32 @@ # To view a copy of this license, visit http://creativecommons.org/licenses/by-sa/4.0/. from pathlib import Path -import sys import gprMax -import numpy as np # file path step fn = Path(__file__) parts = fn.parts -# subgrid Discretisation is 1 mm in x, y, z directions. This allows us -# to model the geometry of the antenna +# Subgrid Discretisation in x, y, z directions. dl_s = 1e-3 -# subgridding ratio. This must always be an odd integer multiple. In this case -# the main grid discrestisation is 9e-3 m. + +# Subgridding ratio. This must always be an odd integer multiple. ratio = 5 dl = dl_s * ratio -# cells -# default number of pml cells +# Cells +# Default number of PML cells pml_cells = 10 -# distance between model and pml cells +# Distance between model and PML cells pml_gap = 15 -# number of cells between the Inner Surface and the Outer Surface of the sub-grid +# Number of cells between the Inner Surface and the Outer Surface of the sub-grid is_os_gap = 4 -# size of the sub-gridded region +# Size of the sub-gridded region sub_gridded_region = 3 -# domain size +# Domain size extent = sub_gridded_region + 2 * (pml_cells + pml_gap + is_os_gap) -# domain extent +# Domain extent x = dl * extent y = x z = x @@ -65,20 +62,20 @@ sg_p1 = [sg_x1, sg_y1, sg_z1] sg = gprMax.SubGridHSG(p1=sg_p0, p2=sg_p1, ratio=ratio, id='mysubgrid') scene.add(sg) -# plastic box in sub grid +# Plastic box in sub grid material = gprMax.Material(er=3, mr=1, se=0, sm=0, id='plastic') scene.add(material) plastic_box = gprMax.Box(p1=(30*dl, 30*dl, 30*dl), p2=(31*dl, 31*dl, 31*dl), material_id='plastic') sg.add(plastic_box) -# create a geometry view of the sub grid only. This command currently exports the entire subgrid regardless of p1, p2 +# Create a geometry view of the sub grid only. This command currently exports the entire subgrid regardless of p1, p2 gv_sg_normal = gprMax.GeometryView(p1=sg_p0, p2=sg_p1, dl=(1e-3, 1e-3, 1e-3), filename=fn.with_suffix('').parts[-1] + '_subgrid_normal', output_type='n') -# add the subgrid geometry view to the sub grid object +# Add the subgrid geometry view to the sub grid object sg.add(gv_sg_normal) gprMax.run(scenes=[scene], n=1, geometry_only=False, outputfile=fn, subgrid=True, autotranslate=True) diff --git a/tests/__init__.py b/testing/__init__.py similarity index 100% rename from tests/__init__.py rename to testing/__init__.py diff --git a/tests/analytical_solutions.py b/testing/analytical_solutions.py similarity index 100% rename from tests/analytical_solutions.py rename to testing/analytical_solutions.py diff --git a/tests/benchmarking/__init__.py b/testing/benchmarking/__init__.py similarity index 100% rename from tests/benchmarking/__init__.py rename to testing/benchmarking/__init__.py diff --git 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toolboxes/STLtoVoxel/examples/stl/point_cloud/mont_zusphite.ply diff --git a/user_libs/STLtoVoxel/license.md b/toolboxes/STLtoVoxel/license.md similarity index 100% rename from user_libs/STLtoVoxel/license.md rename to toolboxes/STLtoVoxel/license.md diff --git a/user_libs/STLtoVoxel/perimeter.py b/toolboxes/STLtoVoxel/perimeter.py similarity index 100% rename from user_libs/STLtoVoxel/perimeter.py rename to toolboxes/STLtoVoxel/perimeter.py diff --git a/user_libs/STLtoVoxel/slice.py b/toolboxes/STLtoVoxel/slice.py similarity index 100% rename from user_libs/STLtoVoxel/slice.py rename to toolboxes/STLtoVoxel/slice.py diff --git a/user_libs/STLtoVoxel/stltovoxel.py b/toolboxes/STLtoVoxel/stltovoxel.py similarity index 100% rename from user_libs/STLtoVoxel/stltovoxel.py rename to toolboxes/STLtoVoxel/stltovoxel.py diff --git a/tools/HPC_scripts/gprmax_omp.sh b/toolboxes/Utilities/HPC/gprmax_omp.sh similarity index 100% rename from tools/HPC_scripts/gprmax_omp.sh rename to 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b/toolboxes/Utilities/MATLAB/plot_Ascan.m similarity index 100% rename from tools/MATLAB_scripts/plot_Ascan.m rename to toolboxes/Utilities/MATLAB/plot_Ascan.m diff --git a/tools/MATLAB_scripts/plot_Bscan.m b/toolboxes/Utilities/MATLAB/plot_Bscan.m similarity index 100% rename from tools/MATLAB_scripts/plot_Bscan.m rename to toolboxes/Utilities/MATLAB/plot_Bscan.m diff --git a/tools/Paraview macros/gprMax.py b/toolboxes/Utilities/Paraview/gprMax.py similarity index 100% rename from tools/Paraview macros/gprMax.py rename to toolboxes/Utilities/Paraview/gprMax.py diff --git a/tools/convert_png2h5.py b/toolboxes/Utilities/convert_png2h5.py similarity index 100% rename from tools/convert_png2h5.py rename to toolboxes/Utilities/convert_png2h5.py diff --git a/tools/get_host_spec.py b/toolboxes/Utilities/get_host_spec.py similarity index 100% rename from tools/get_host_spec.py rename to toolboxes/Utilities/get_host_spec.py diff --git a/tools/inputfile_old2new.py b/toolboxes/Utilities/inputfile_old2new.py similarity index 100% rename from tools/inputfile_old2new.py rename to toolboxes/Utilities/inputfile_old2new.py diff --git a/tools/outputfiles_merge.py b/toolboxes/Utilities/outputfiles_merge.py similarity index 100% rename from tools/outputfiles_merge.py rename to toolboxes/Utilities/outputfiles_merge.py diff --git a/user_libs/STLtoVoxel/__init__.py b/toolboxes/__init__.py similarity index 100% rename from user_libs/STLtoVoxel/__init__.py rename to toolboxes/__init__.py diff --git a/user_libs/__init__.py b/user_libs/__init__.py deleted file mode 100644 index e69de29b..00000000 diff --git a/user_models/antenna_like_GSSI_400_fs.py b/user_models/antenna_like_GSSI_400_fs.py deleted file mode 100644 index a6481d25..00000000 --- a/user_models/antenna_like_GSSI_400_fs.py +++ /dev/null @@ -1,35 +0,0 @@ -from pathlib import Path - -import gprMax -from user_libs.GPRAntennaModels.GSSI import antenna_like_GSSI_400 - -# File path for output -fn = Path(__file__) - -# Discretisation -dl = 0.001 - -# Domain -x = 0.380 -y = 0.380 -z = 0.360 - -scene = gprMax.Scene() - -title = gprMax.Title(name=fn.with_suffix('').name) -domain = gprMax.Domain(p1=(x, y, z)) -dxdydz = gprMax.Discretisation(p1=(dl, dl, dl)) -time_window = gprMax.TimeWindow(time=12e-9) - -scene.add(title) -scene.add(domain) -scene.add(dxdydz) -scene.add(time_window) - -# Import antenna model and add to model -gssi_objects = antenna_like_GSSI_400(0.190, 0.190, 0.140, resolution=dl) -for obj in gssi_objects: - scene.add(obj) - -# Run model -gprMax.run(scenes=[scene], geometry_only=False, outputfile=fn) diff --git a/user_models/antenna_like_MALA_1200_fs.py b/user_models/antenna_like_MALA_1200_fs.py deleted file mode 100644 index f3eb08e1..00000000 --- a/user_models/antenna_like_MALA_1200_fs.py +++ /dev/null @@ -1,35 +0,0 @@ -from pathlib import Path - -import gprMax -from user_libs.GPRAntennaModels.MALA import antenna_like_MALA_1200 - -# File path for output -fn = Path(__file__) - -# Discretisation -dl = 0.001 - -# Domain -x = 0.264 -y = 0.189 -z = 0.220 - -scene = gprMax.Scene() - -title = gprMax.Title(name=fn.with_suffix('').name) -domain = gprMax.Domain(p1=(x, y, z)) -dxdydz = gprMax.Discretisation(p1=(dl, dl, dl)) -time_window = gprMax.TimeWindow(time=6e-9) - -scene.add(title) -scene.add(domain) -scene.add(dxdydz) -scene.add(time_window) - -# Import antenna model and add to model -mala_objects = antenna_like_MALA_1200(0.132, 0.095, 0.100, resolution=dl) -for obj in mala_objects: - scene.add(obj) - -# Run model -gprMax.run(scenes=[scene], geometry_only=False, outputfile=fn) diff --git a/user_models/antenna_wire_dipole_fs.vtp b/user_models/antenna_wire_dipole_fs.vtp deleted file mode 100644 index 1a95df72..00000000 Binary files a/user_models/antenna_wire_dipole_fs.vtp and /dev/null differ diff --git a/user_models/rtm/bgr_6.mat b/user_models/rtm/bgr_6.mat deleted file mode 100644 index 2e266149..00000000 Binary files a/user_models/rtm/bgr_6.mat and /dev/null differ diff --git a/user_models/rtm/rtm.py b/user_models/rtm/rtm.py deleted file mode 100644 index 60160eb1..00000000 --- a/user_models/rtm/rtm.py +++ /dev/null @@ -1,174 +0,0 @@ -from pathlib import Path - -import gprMax -import h5py -import matplotlib.pyplot as plt -import numpy as np -from scipy.constants import c -from scipy.io import loadmat - - -# Title and file path for FDTD model output -modeltitle = 'bgr_6' -fn = Path(__file__) -fn = Path(fn.parent, modeltitle) - -# Load B-scan data to be migrated -matfile = Path(str(Path(__file__).parent.resolve()), modeltitle + '.mat') -matcontents = loadmat(str(matfile)) -data = matcontents['data'] -data = np.transpose(data) # Transpose to rows: samples, cols: traces - -# Specify trace interval, sampling interval, & create time vector for B-scan data -trac_int = 0.005 # metres -samp_int = 1.7578e-11 # seconds -maxtime = samp_int * data.shape[0] -time = np.linspace(0, maxtime, data.shape[0]) - -# Specify velocity/permittivity of B-scan data -v = 0.12e9 - -# Depth used for calculating FDTD z-dimension -depth = v * maxtime / 2 - -# FDTD discretisation, 2D domain dims, and time window -dl = 0.001 # metres -pml_cells = 10 -extra_cells = 10 # Allow some extra cells after PML before placing sources -x_cells = data.shape[1] + 2 * pml_cells + 2 * extra_cells -x = x_cells * trac_int -y_cells = 1 -y = y_cells * dl -z_cells = int(np.ceil(depth / dl) + 2 * pml_cells + 2 * extra_cells) -z = z_cells * dl - -# Can build FDTD model from: -# 1. Matrix of velocity/permittivity, then write to file, and import -# 2. Directly using geometry primitives, i.e. boxes, etc... - -# Option 1: -# Holds permittivity field to import into FDTD model -# er = np.ones((x_cells, y_cells, z_cells - (pml_cells + extra_cells))) -# er_value = np.around(4 * (c / v)**2, decimals=2) # 4xEr as velocity doubled -# er = er * er_value -# mat_ers = np.unique(er) - -# Write materials text file -# with open(fn.with_suffix('.txt'), 'w') as fmaterials: -# for i, mat_er in enumerate(mat_ers): -# er[er==mat_er] = i -# fmaterials.write(f'#material: {mat_er} 0 1 0 mat{i}\n') - -# # Write permittivity HDF5 file -# with h5py.File(fn.with_suffix('.h5'), 'w') as fdata: -# fdata.attrs['Title'] = modeltitle -# fdata.attrs['dx_dy_dz'] = (dl, dl, dl) -# fdata['/data'] = er.astype('int16') - -# Build FDTD model -scene = gprMax.Scene() - -title = gprMax.Title(name=modeltitle) -domain = gprMax.Domain(p1=(x, y, z)) -dxdydz = gprMax.Discretisation(p1=(dl, dl, dl)) -time_window = gprMax.TimeWindow(time=maxtime) - -scene.add(title) -scene.add(domain) -scene.add(dxdydz) -scene.add(time_window) - -# Option 1 -# go = gprMax.GeometryObjectsRead(p1=(0, 0, 0), geofile=fn.with_suffix('.h5'), -# matfile=fn.with_suffix('.txt')) -# scene.add(go) - -# Option 2 -mat = gprMax.Material(er=np.around(4 * (c / v)**2, decimals=2), se=0, mr=1, - sm=0, id='mat1') -scene.add(mat) -b1 = gprMax.Box(p1=(0, 0, 0), p2=(domain.props.p1[0], dl, - domain.props.p1[2] - (pml_cells + extra_cells) * dl), - material_id='mat1') -scene.add(b1) - -# Specify waveforms and sources from reversed B-scan data -for i in range(data.shape[1]): - wv = gprMax.Waveform(wave_type='user', - user_values=np.flipud(data[:,i]), user_time=time, - kind='linear', fill_value='extrapolate', - id='mypulse' + str(i + 1)) - scene.add(wv) - src = gprMax.HertzianDipole(polarisation='y', - p1=((pml_cells + extra_cells) * dl + i * trac_int, - 0, domain.props.p1[2] - (pml_cells + extra_cells) * dl), - waveform_id='mypulse' + str(i + 1)) - scene.add(src) - -gv = gprMax.GeometryView(p1=(0, 0, 0), p2=domain.props.p1, dl=(dl, dl, dl), - filename=fn.with_suffix('').parts[-1], - output_type='n') - -# Snapshot at end of time window is RTM result -fileext = '.h5' # Can also be '.vti' for a VTK format -snap = gprMax.Snapshot(p1=((pml_cells + extra_cells) * dl, - 0, - (pml_cells + extra_cells) * dl), - p2=(domain.props.p1[0] - (pml_cells + extra_cells) * dl, - dl, - domain.props.p1[2] - (pml_cells + extra_cells) * dl), - dl=(dl, dl, dl), - filename=fn.with_suffix('').parts[-1] + '_rtm_result', - fileext=fileext, time=maxtime) - -scene.add(gv) -scene.add(snap) - -# Run FDTD model -gprMax.run(scenes=[scene], n=1, geometry_only=False, outputfile=fn) - -# Open RTM results file -filename = Path(str(fn) + '_snaps', fn.with_suffix('').parts[-1] + '_rtm_result' + fileext) -fieldcomponent = 'Ey' -with h5py.File(filename, 'r') as f: - outputdata = f[fieldcomponent] - outputdata = np.array(outputdata) - time = f.attrs['time'] - -# Manipulation/processing of outputdata -outputdata = outputdata.squeeze() -outputdata = outputdata.transpose() - -# Plot RTM result -fig, (ax1, ax2) = plt.subplots(nrows=2, ncols=1, num=str(filename), - figsize=(15, 10), facecolor='w', edgecolor='w') -orig_plt = ax1.imshow(data, extent=[0, data.shape[1] * trac_int, - (data.shape[0] * samp_int) / 2 * v, 0], interpolation='nearest', - aspect='auto', cmap='viridis', vmin=-np.amax(np.abs(data)), - vmax=np.amax(np.abs(data))) -ax1.set_xlabel('Distance [m]') -ax1.set_ylabel('Depth [m]') -ax1.title.set_text('Original') -ax1.grid(which='both', axis='both', linestyle='-.') -cb1 = plt.colorbar(orig_plt, ax=ax1) -cb1.set_label(fieldcomponent + ' [V/m]') - -rtm_plt = ax2.imshow(np.flipud(outputdata), - extent=[0, outputdata.shape[1] * dl, depth, 0], - interpolation='nearest', aspect='auto', cmap='viridis', - vmin=-np.amax(np.abs(outputdata)), - vmax=np.amax(np.abs(outputdata))) -ax2.set_xlabel('Distance [m]') -ax2.set_ylabel('Depth [m]') -ax2.title.set_text('RTM') -ax2.grid(which='both', axis='both', linestyle='-.') -cb2 = plt.colorbar(rtm_plt, ax=ax2) -cb2.set_label(fieldcomponent + ' [V/m]') - -# Save a PDF/PNG of the figure -# fig.savefig(filename.with_suffix('.pdf'), dpi=None, format='pdf', -# bbox_inches='tight', pad_inches=0.1) -# fig.savefig(filename.with_suffix('.png'), dpi=150, format='png', -# bbox_inches='tight', pad_inches=0.1) - -plt.show() \ No newline at end of file