Correcting toolbox names

docs/source/conf.py

@@ -62,7 +62,7 @@ master_doc = 'index'
 
 # General information about the project.
 project = 'gprMax'
-copyright = '2015-2023, The University of Edinburgh, United Kingdom. Authors: Craig Warren, Antonis Giannopoulos, and John Hartley'
+copyright = f'2015-{time.strftime("%Y")}, The University of Edinburgh, United Kingdom. Authors: Craig Warren, Antonis Giannopoulos, and John Hartley'
 author = 'Craig Warren, Antonis Giannopoulos, and John Hartley'
 
 # The version info for the project you're documenting, acts as replacement for

toolboxes/AntennaPatterns/README.rst

@@ -26,26 +26,26 @@ The package contains scripts to help calculate, process, and visualise field pat
 Package contents
 ================
 
-* ``initial_save.py`` is a module that calculates and stores (in a Numpy file) the field patterns from the output file of a simulation.
-* ``plot_fields.py`` is a module that plots the field patterns. It should be used after the field pattern data has been processed and stored using the ``initial_save.py`` module.
+* `initial_save.py` is a module that calculates and stores (in a Numpy file) the field patterns from the output file of a simulation.
+* `plot_fields.py` is a module that plots the field patterns. It should be used after the field pattern data has been processed and stored using the `initial_save.py` module.
 
-The package has been designed to work with input files that follow examples found in the ``user_models`` directory:
+The package has been designed to work with input files found in the `examples` directory:
 
-* ``antenna_like_GSSI_1500_patterns_E.in`` is an input file that includes an antenna model similar to a GSSI 1.5 GHz antenna and receivers to calculate a field pattern in the principal E-plane of the antenna
-* ``antenna_like_GSSI_1500_patterns_H.in`` is an input file that includes an antenna model similar to a GSSI 1.5 GHz antenna and receivers to calculate a field pattern in the principal H-plane of the antenna
+* `antenna_like_GSSI_1500_patterns_E.in` is an input file that includes an antenna model similar to a GSSI 1.5 GHz antenna and receivers to calculate a field pattern in the principal E-plane of the antenna
+* `antenna_like_GSSI_1500_patterns_H.in` is an input file that includes an antenna model similar to a GSSI 1.5 GHz antenna and receivers to calculate a field pattern in the principal H-plane of the antenna
 
 
 How to use the package
 ======================
 
 * Firstly you should familiarise yourself with the example model input file. Edit the input file as desired and run one of the simulations for either E-plane or H-plane patterns.
-* Whilst the simulation is running edit the 'user configurable parameters' sections of the ``initial_save.py`` and ``plot_fields.py`` modules to match the setup of the simulation.
-* Once the simulation has completed, run the ``initial_save.py`` module on the output file, e.g. for the E-plane ``python -m user_libs.AntennaPatterns.initial_save user_models/antenna_like_GSSI_1500_patterns_E_Er5.h5``. This will produce a Numpy file containing the field pattern data.
-* Plot the field pattern data by running the ``plot_fields.py`` module on the Numpy file, e.g. for the E-plane ``python -m user_libs.AntennaPatterns.plot_fields user_models/antenna_like_GSSI_1500_patterns_E_Er5.npy``
+* Whilst the simulation is running edit the 'user configurable parameters' sections of the `initial_save.py` and `plot_fields.py` modules to match the setup of the simulation.
+* Once the simulation has completed, run the `initial_save.py` module on the output file, e.g. for the E-plane `python -m toolboxes.AntennaPatterns.initial_save examples/antenna_like_GSSI_1500_patterns_E_Er5.h5`. This will produce a Numpy file containing the field pattern data.
+* Plot the field pattern data by running the `plot_fields.py` module on the Numpy file, e.g. for the E-plane `python -m toolboxes.AntennaPatterns.plot_fields examples/antenna_like_GSSI_1500_patterns_E_Er5.npy`
 
 .. tip::
 
-    If you want to create different plots you just need to edit and re-run the ``plot_fields.py`` module on the Numpy file, i.e. you don't have to re-process the output file.
+    If you want to create different plots you just need to edit and re-run the `plot_fields.py` module on the Numpy file, i.e. you don't have to re-process the output file.
 
 
 .. figure:: ../../images_shared/antenna_like_GSSI_1500_patterns_E_Er5.png

toolboxes/AustinManWoman/README.rst

@@ -15,7 +15,7 @@ Information
 
 **Attribution/cite**: Please follow the instructions at http://web.corral.tacc.utexas.edu/AustinManEMVoxels/AustinMan/citing_the_model/index.html
 
-`AustinMan and AustinWoman <http://bit.ly/AustinMan>`_ are open source electromagnetic voxel models of the human body, which are developed by the `Computational Electromagnetics Group <http://www.ece.utexas.edu/research/areas/electromagnetics-acoustics>`_ at `The University of Texas at Austin <http://www.utexas.edu>`_. The models are based on data from the `National Library of Medicine’s Visible Human Project <https://www.nlm.nih.gov/research/visible/visible_human.html>`_.
+`AustinMan and AustinWoman <https://web.corral.tacc.utexas.edu/AustinManEMVoxels/AustinMan/index.html>`_ are open source electromagnetic voxel models of the human body, which are developed by the `Computational Electromagnetics Group <http://www.ece.utexas.edu/research/areas/ea>`_ at `The University of Texas at Austin <http://www.utexas.edu>`_. The models are based on data from the `National Library of Medicine’s Visible Human Project <https://www.nlm.nih.gov/research/visible/visible_human.html>`_.
 
 .. figure:: ../../images_shared/AustinMan_head.png
     :width: 600 px
@@ -46,22 +46,22 @@ Package contents
     AustinManWoman_materials_dispersive.txt
     head_only_h5.py
 
-* ``AustinManWoman_materials.txt`` is a text file containing `non-dispersive material properties at 900 MHz <http://niremf.ifac.cnr.it/tissprop/>`_.
-* ``AustinManWoman_materials_dispersive.txt`` is a text file containing `dispersive material properties using a 3-pole Debye model <http://dx.doi.org/10.1109/LMWC.2011.2180371>`_.
+* `AustinManWoman_materials.txt` is a text file containing `non-dispersive material properties at 900 MHz <http://niremf.ifac.cnr.it/tissprop/>`_.
+* `AustinManWoman_materials_dispersive.txt` is a text file containing `dispersive material properties using a 3-pole Debye model <http://dx.doi.org/10.1109/LMWC.2011.2180371>`_.
 
 .. note::
 
     * 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.
 
-* `Download a HDF5 file (.h5) of AustinMan or AustinWoman <http://bit.ly/AustinMan>`_ at the resolution you wish to use
+* `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
 
 To insert either AustinMan or AustinWoman models into a simulation use the ``#geometry_objects_read``.
 
@@ -72,9 +72,9 @@ To insert a 2x2x2mm :math:`^3` AustinMan with the lower left corner 40mm from th
 
 .. code-block:: none
 
-    #geometry_objects_read: 0.04 0.04 0.04 ../user_libs/AustinManWoman/AustinMan_v2.3_2x2x2.h5 ../user_libs/AustinManWoman/AustinManWoman_materials_dispersive.txt
+    #geometry_objects_read: 0.04 0.04 0.04 ../toolboxes/AustinManWoman/AustinMan_v2.3_2x2x2.h5 ../toolboxes/AustinManWoman/AustinManWoman_materials_dispersive.txt
 
-For further information on the ``#geometry_objects_read`` see the section on object contruction commands in the :ref:`Input commands section <commands>`.
+For further information on the `#geometry_objects_read` see the section on object contruction commands in the :ref:`Input commands section <commands>`.
 
 .. figure:: ../../images_shared/AustinMan.png
     :width: 300 px

toolboxes/DebyeFit/README.rst

@@ -47,14 +47,14 @@ Package contents
 
 There are two main scripts:
 
-* ```Debye_fit.py``` contains definitions of all Relaxation functions classes
-* ```optimization.py``` contains definitions of three choosen global optimization methods
+* ``Debye_fit.py`` contains definitions of all Relaxation functions classes
+* ``optimization.py`` contains definitions of three choosen global optimization methods
 
 
 Relaxation Class
 ----------------
 
-This class is designed for modelling different relaxation functions, like Havriliak-Negami (```HavriliakNegami```), Jonscher (```Jonscher```), Complex Refractive Index Mixing (```CRIM```) models, and arbitrary dielectric data derived experimentally or calculated using some other function (```Rawdata```).
+This class is designed for modelling different relaxation functions, like Havriliak-Negami (``HavriliakNegami``), Jonscher (``Jonscher``), Complex Refractive Index Mixing (`CRIM`) models, and arbitrary dielectric data derived experimentally or calculated using some other function (``Rawdata``).
 
 More about the ``Relaxation`` class structure can be found in the :doc:`Relaxation doc <relaxation.rst>`.