Copyright and package name updates

testing/analytical_solutions.py

@@ -1,4 +1,4 @@
-# Copyright (C) 2015-2022: The University of Edinburgh, United Kingdom
+# Copyright (C) 2015-2023: The University of Edinburgh, United Kingdom
 #                 Authors: Craig Warren, Antonis Giannopoulos, and John Hartley
 #
 # This file is part of gprMax.

testing/models_pmls/plot_pml_comparison.py

@@ -1,4 +1,4 @@
-# Copyright (C) 2015-2022: The University of Edinburgh, United Kingdom
+# Copyright (C) 2015-2023: The University of Edinburgh, United Kingdom
 #                 Authors: Craig Warren, Antonis Giannopoulos, and John Hartley
 #
 # This file is part of gprMax.

testing/test_experimental.py

@@ -1,4 +1,4 @@
-# Copyright (C) 2015-2022: The University of Edinburgh, United Kingdom
+# Copyright (C) 2015-2023: The University of Edinburgh, United Kingdom
 #                 Authors: Craig Warren, Antonis Giannopoulos, and John Hartley
 #
 # This file is part of gprMax.

testing/test_models.py

@@ -1,4 +1,4 @@
-# Copyright (C) 2015-2022: The University of Edinburgh, United Kingdom
+# Copyright (C) 2015-2023: The University of Edinburgh, United Kingdom
 #                 Authors: Craig Warren, Antonis Giannopoulos, and John Hartley
 #
 # This file is part of gprMax.

toolboxes/AustinManWoman/README.rst

@@ -22,7 +22,7 @@ Information
 
     FDTD geometry mesh showing the head of the AustinMan model (2x2x2mm :math:`^3`).
 
-The following whole body models are available.
+The following whole body models are available:
 
 =========== ========================== ==================
 Model       Resolution (mm :math:`^3`) Dimensions (cells)
@@ -54,12 +54,12 @@ Package contents
     * The main body tissues are described using a 3-pole Debye model, but not all materials have a dispersive description.
     * The dispersive material properties can only be used with the 1x1x1mm or 2x2x2mm AustinMan/Woman models. This is because the time step of the model must always be less than any of the relaxation times of the poles of the Debye models used for the dispersive material properties.
 
-* `head_only_h5.py` is a script to assist with creating a model of only the head from a full body AustinMan/Woman model.
+* ``head_only_h5.py`` is a script to assist with creating a model of only the head from a full body AustinMan/Woman model.
 
 How to use the package
 ======================
 
-The AustinMan and AustinWoman models themselves are not included in the user libraries sub-package.
+The AustinMan and AustinWoman models themselves are not included in this sub-package.
 
 * `Download a HDF5 file (.h5) of AustinMan or AustinWoman <https://web.corral.tacc.utexas.edu/AustinManEMVoxels/AustinMan/download/index.html>`_ at the resolution you wish to use
 

toolboxes/DebyeFit/README.rst

@@ -125,7 +125,7 @@ The ``Jonscher`` class has the following structure:
 * ``f_min`` is first bound of the frequency range used to approximate the given function (Hz),
 * ``f_max`` is second bound of the frequency range used to approximate the given function (Hz),
 * ``e_inf`` is a real part of relative permittivity at infinite frequency,
-* ``a_p``` is a Jonscher parameter. Real positive float number,
+* ``a_p`` is a Jonscher parameter. Real positive float number,
 * ``omega_p`` is a Jonscher parameter. Real positive float number,
 * ``n_p`` Jonscher parameter, 0 < n_p < 1.
 
@@ -183,7 +183,7 @@ Class Optimizer
 ---------------
 
 This class supports global optimization algorithms (particle swarm, dual annealing, evolutionary algorithms) for finding an optimal set of relaxation times that minimise the error between the actual and the approximated electric permittivity, and calculates optimised weights for the given relaxation times.
-Code written here is mainly based on external libraries, like ```scipy``` and ```pyswarm```.
+Code written here is mainly based on external libraries, like ``scipy`` and ``pyswarm``.
 
 More about the ``Optimizer`` class structure can be found in the :doc:`Optimisation doc <optimisation.rst>`.
 
@@ -216,12 +216,12 @@ How to use the package
 Examples
 --------
 
-In the examples directory you will find Jupyter notebooks, scripts, and data that demonstrate different cases of how to use the main script ```DebyeFit.py```:
+In the examples directory you will find Jupyter notebooks, scripts, and data that demonstrate different cases of how to use the main script ``DebyeFit.py``:
 
-* ```example_DebyeFitting.ipynb```: simple cases of using all available implemented relaxation functions,
-* ```example_BiologicalTissues.ipynb```: simple cases of using Cole-Cole function for biological tissues,
-* ```example_ColeCole.py```: simple cases of using Cole-Cole function in case of 3, 5 and automatically chosen number of Debye poles,
-* ```Test.txt```: raw data for testing ```Rawdata``` class, file contains 3 columns: the first column contains the frequencies (Hz) associated with the value of the permittivity; the second column contains the real part of the relative permittivity; and the third column contains the imaginary part of the relative permittivity.
+* ``example_DebyeFitting.ipynb``: simple cases of using all available implemented relaxation functions,
+* ``example_BiologicalTissues.ipynb``: simple cases of using Cole-Cole function for biological tissues,
+* ``example_ColeCole.py``: simple cases of using Cole-Cole function in case of 3, 5 and automatically chosen number of Debye poles,
+* ``Test.txt``: raw data for testing ``Rawdata`` class, file contains 3 columns: the first column contains the frequencies (Hz) associated with the value of the permittivity; the second column contains the real part of the relative permittivity; and the third column contains the imaginary part of the relative permittivity.
 
 The following code shows a basic example of how to use the Havriliak-Negami function:
 

toolboxes/GPRAntennaModels/README.rst

@@ -50,7 +50,7 @@ To include an antenna model similar to a GSSI 1.5 GHz antenna at a location 0.12
 .. code-block:: none
 
     #python:
-    from user_libs.GPRAntennaModels.GSSI import antenna_like_GSSI_1500
+    from toolboxes.GPRAntennaModels.GSSI import antenna_like_GSSI_1500
     antenna_like_GSSI_1500(0.125, 0.094, 0.100, resolution=0.002)
     #end_python:
 

toolboxes/LandmineModels/README.rst

@@ -71,7 +71,7 @@ The input file for inserting the PMN landmine, with the lower left corner 10mm f
     #domain: 0.136 0.176 0.070
     #dx_dy_dz: 0.001 0.001 0.001
     #time_window: 5e-9
-    #geometry_objects_read: 0.010 0.010 0.010 ../user_libs/LandmineModels/PMN_1x1x1.h5 ../user_libs/LandmineModels/PMN_materials.txt
+    #geometry_objects_read: 0.010 0.010 0.010 ../toolboxes/LandmineModels/PMN_1x1x1.h5 ../toolboxes/LandmineModels/PMN_materials.txt
     #geometry_view: 0 0 0 0.136 0.176 0.070 0.001 0.001 0.001 landmine_PMN_fs n
 
 For further information on the ``#geometry_objects_read`` see the section on object contruction commands in the :ref:`Input commands section <commands>`.

toolboxes/Materials/README.rst

@@ -21,7 +21,7 @@ The simplest way to access any of the material libraries is to use the ``#includ
 
 .. code-block:: none
 
-    #include_file: user_libs/Materials/eccosorb.txt
+    #include_file: toolboxes/Materials/eccosorb.txt
     #box: 0 0 0 0.5 0.5 0.5 eccosorb_ls22
 
 Eccosorb

toolboxes/Plotting/plot_Ascan.py

@@ -1,4 +1,4 @@
-# Copyright (C) 2015-2022: The University of Edinburgh, United Kingdom
+# Copyright (C) 2015-2023: The University of Edinburgh, United Kingdom
 #                 Authors: Craig Warren, Antonis Giannopoulos, and John Hartley
 #
 # This file is part of gprMax.

toolboxes/Plotting/plot_Bscan.py

@@ -1,4 +1,4 @@
-# Copyright (C) 2015-2022: The University of Edinburgh, United Kingdom
+# Copyright (C) 2015-2023: The University of Edinburgh, United Kingdom
 #                 Authors: Craig Warren, Antonis Giannopoulos, and John Hartley
 #
 # This file is part of gprMax.

toolboxes/Plotting/plot_antenna_params.py

@@ -1,4 +1,4 @@
-# Copyright (C) 2015-2022: The University of Edinburgh, United Kingdom
+# Copyright (C) 2015-2023: The University of Edinburgh, United Kingdom
 #                 Authors: Craig Warren, Antonis Giannopoulos, and John Hartley
 #
 # This file is part of gprMax.

toolboxes/Plotting/plot_source_wave.py

@@ -1,4 +1,4 @@
-# Copyright (C) 2015-2022: The University of Edinburgh, United Kingdom
+# Copyright (C) 2015-2023: The University of Edinburgh, United Kingdom
 #                 Authors: Craig Warren, Antonis Giannopoulos, and John Hartley
 #
 # This file is part of gprMax.

toolboxes/STLtoVoxel/README.rst

@@ -43,7 +43,7 @@ To create a voxelised mesh (HDF5 geometry file) from the ubiquitous `Stanford bu
 
 .. code-block:: none
 
-    python -m user_libs.STLtoVoxel.stltovoxel user_libs/STLtoVoxel/examples/stl/Stanford_Bunny.stl -matindex 2 -dxdydz 0.001 0.001 0.001
+    python -m toolboxes.STLtoVoxel.stltovoxel toolboxes/STLtoVoxel/examples/stl/Stanford_Bunny.stl -matindex 2 -dxdydz 0.001 0.001 0.001
 
 Since the number of voxels are 108 x 88 108 and the spatial discretisation chosen is 1mm, the physical dimensions of the Stanford bunny when imported into gprMax will be 0.108 x 0.088 x 0.108mm.
 

toolboxes/Utilities/MATLAB/README.rst

@@ -1 +0,0 @@
-These MATLAB scripts are designed as a base to help you get started with plotting data (A-scans and B-scans) from simulations. They do not feature extensive error checking.

toolboxes/Utilities/Paraview/gprMax.py

@@ -1,4 +1,4 @@
-# Copyright (C) 2015-2022: The University of Edinburgh, United Kingdom
+# Copyright (C) 2015-2023: The University of Edinburgh, United Kingdom
 #                 Authors: Craig Warren, Antonis Giannopoulos, and John Hartley
 #
 # This file is part of gprMax.

toolboxes/Utilities/README.rst

@@ -1 +1,20 @@
-These MATLAB scripts are designed as a base to help you get started with plotting data (A-scans and B-scans) from simulations. They do not feature extensive error checking.
+Toolboxes is a sub-package where useful Python modules contributed by users are stored.
+
+*********
+Utilities
+*********
+
+Information
+===========
+
+This package contains various scripts and helper functions.
+
+Package contents
+================
+
+* ``HPC`` is a folder with scripts to assist with running gprMax on high-performance computing (HPC) systems.
+* ``MATLAB`` is a folder containing scripts are designed as a base to help getting started with plotting data (A-scans and B-scans) from simulations. They do not feature extensive error checking.
+* ``Paraview.py`` is a folder containing a Python macro to be installed into Paraview. The macro enables materials to be easily visualised when geometry files are loaded into Paraview.
+* ``convert_png2h5.py`` is a script to convert a PNG image to a HDF5 file that can be used to import geometry (#geometry_objects_read) into a 2D model.
+* ``get_host_spec.py`` is a script that prints information about the host machine capabilities for OpenMP/CUDA/OpenCL.
+* ``outputfiles_merge.py`` is a script that merges traces (A-scans) from multiple output files into one new file, then optionally removes the series of output files.

toolboxes/Utilities/convert_png2h5.py

@@ -1,4 +1,4 @@
-# Copyright (C) 2015-2022: The University of Edinburgh, United Kingdom
+# Copyright (C) 2015-2023: The University of Edinburgh, United Kingdom
 #                 Authors: Craig Warren, Antonis Giannopoulos, and John Hartley
 #
 # This file is part of gprMax.

toolboxes/Utilities/get_host_spec.py

@@ -1,4 +1,4 @@
-# Copyright (C) 2015-2022: The University of Edinburgh, United Kingdom
+# Copyright (C) 2015-2023: The University of Edinburgh, United Kingdom
 #                 Authors: Craig Warren, Antonis Giannopoulos, and John Hartley
 #
 # This file is part of gprMax.

toolboxes/Utilities/outputfiles_merge.py

@@ -1,4 +1,4 @@
-# Copyright (C) 2015-2022: The University of Edinburgh, United Kingdom
+# Copyright (C) 2015-2023: The University of Edinburgh, United Kingdom
 #                 Authors: Craig Warren, Antonis Giannopoulos, and John Hartley
 #
 # This file is part of gprMax.