Moved images to shared directory at top-level

README.rst

@@ -4,7 +4,7 @@
 
 |
 
-.. image:: docs/source/images/gprMax_logo_small.png
+.. image:: ../../images_shared/gprMax_logo_small.png
     :target: http://www.gprmax.com
 
 ***************

docs/source/coding.rst

@@ -14,6 +14,6 @@ OpenMP which enables it to run on multi-core CPUs. gprMax also features a
 Messaging Passing Interface (MPI) task farm, which can operate with CPU nodes or
 multiple GPUs.
 
-.. figure:: images/code_overview.png
+.. figure:: ../../images_shared/code_overview.png
 
     Basic, high-level overview of the flow of control (operation) of the code.

docs/source/conf.py

@@ -144,7 +144,7 @@ html_title = 'gprMax User Guide'
 
 # The name of an image file (relative to this directory) to place at the top
 # of the sidebar.
-# html_logo = 'images/gprMax_FB_logo.png'
+html_logo = '../../images_shared/gprMax_FB_logo.png'
 
 # The name of an image file (within the static path) to use as favicon of the
 # docs.  This file should be a Windows icon file (.ico) being 16x16 or 32x32
@@ -246,7 +246,7 @@ latex_documents = [
 
 # The name of an image file (relative to this directory) to place at the top of
 # the title page.
-latex_logo = 'images/gprMax_logo.png'
+latex_logo = '../../images_shared/gprMax_logo.png'
 
 # For "manual" documents, if this is true, then toplevel headings are parts,
 # not chapters.

docs/source/examples_advanced.rst

@@ -15,7 +15,7 @@ This example demonstrates how to build a more realistic soil model using a stoch
     :language: none
     :linenos:
 
-.. figure:: images/heterogeneous_soil.png
+.. figure:: ../../images_shared/heterogeneous_soil.png
     :width: 600 px
 
     FDTD geometry mesh showing a heterogeneous soil model with a rough surface.

docs/source/examples_antennas.rst

@@ -32,21 +32,21 @@ You can view the results (see :ref:`output` and :ref:`tools<plotting>` sections)
 
 .. _antenna_wire_dipole_fs_tl_params:
 
-.. figure:: images/antenna_wire_dipole_fs_tl_params.png
+.. figure:: ../../images_shared/antenna_wire_dipole_fs_tl_params.png
     :width: 600px
 
     Time and frequency domain plots of the incident and total (incident + reflected) voltages and currents in the transmission line (:math:`\Delta f = 17~MHz`).
 
 .. _antenna_wire_dipole_fs_ant_params:
 
-.. figure:: images/antenna_wire_dipole_fs_ant_params.png
+.. figure:: ../../images_shared/antenna_wire_dipole_fs_ant_params.png
     :width: 600px
 
     Input admittance and impedance (resistance and reactance) and s11 parameter values of the antenna (:math:`\Delta f = 17~MHz`).
 
 .. _antenna_wire_dipole_fs_ant_params_detail:
 
-.. figure:: images/antenna_wire_dipole_fs_ant_params_detail.png
+.. figure:: ../../images_shared/antenna_wire_dipole_fs_ant_params_detail.png
     :width: 600px
 
     Detailed view of input admittance and impedance (resistance and reactance) and s11 parameter values of the antenna (:math:`\Delta f = 17~MHz`).
@@ -57,7 +57,7 @@ You can view the results (see :ref:`output` and :ref:`tools<plotting>` sections)
 
 .. _antenna_wire_dipole_fs_ant_params_detail_1p4MHz:
 
-.. figure:: images/antenna_wire_dipole_fs_ant_params_detail_1p4MHz.png
+.. figure:: ../../images_shared/antenna_wire_dipole_fs_ant_params_detail_1p4MHz.png
     :width: 600px
 
     Detailed view of input admittance and impedance (resistance and reactance) and s11 parameter values of the antenna (:math:`\Delta f = 1.4~MHz`)
@@ -76,7 +76,7 @@ This example demonstrates how to use one of the built-in antenna models in a sim
     :language: none
     :linenos:
 
-.. figure:: images/antenna_like_MALA_1200.png
+.. figure:: ../../images_shared/antenna_like_MALA_1200.png
     :width: 600 px
 
     FDTD geometry mesh showing an antenna model similar to a MALA 1.2GHz antenna (skid removed for illustrative purposes).
@@ -96,7 +96,7 @@ When the simulation is run two geometry files for the antenna are produced along
 
 .. _antenna_like_MALA_1200_fs_results:
 
-.. figure:: images/antenna_like_MALA_1200_fs_results.png
+.. figure:: ../../images_shared/antenna_like_MALA_1200_fs_results.png
     :width: 600 px
 
     Ey field output from the receiver bowtie of a model of an antenna similar to a MALA 1.2GHz antenna.
@@ -113,7 +113,7 @@ This example demonstrates how to create a B-scan with an antenna model. The scen
     :language: none
     :linenos:
 
-.. figure:: images/cylinder_Bscan_GSSI_1500.png
+.. figure:: ../../images_shared/cylinder_Bscan_GSSI_1500.png
     :width: 600 px
 
     FDTD geometry mesh showing a metal cylinder buried in a half-space and an antenna model similar to a GSSI 1.5GHz antenna.
@@ -143,7 +143,7 @@ After merging the A-scans into a single file you can now view an image of the B-
 
 .. _cylinder_Bscan_GSSI_1500_results:
 
-.. figure:: images/cylinder_Bscan_GSSI_1500_results.png
+.. figure:: ../../images_shared/cylinder_Bscan_GSSI_1500_results.png
     :width: 600px
 
     B-scan of model of a metal cylinder buried in a dielectric half-space with a model of an antenna similar to a GSSI 1.5GHz antenna.

docs/source/examples_simple_2D.rst

@@ -21,7 +21,7 @@ The geometry of the scenario is straightforward and an image created from the ge
 
 .. _cylinder_half_space_geo:
 
-.. figure:: images/cylinder_half_space_geo.png
+.. figure:: ../../images_shared/cylinder_half_space_geo.png
     :width: 600 px
 
     Geometry of a 2D model of a metal cylinder buried in a dielectric half-space.
@@ -118,7 +118,7 @@ You should have produced an output file ``cylinder_Ascan_2D.h5``. You can view t
 
 .. _cylinder_Ascan_results:
 
-.. figure:: images/cylinder_Ascan_results.png
+.. figure:: ../../images_shared/cylinder_Ascan_results.png
     :width: 600px
 
     Electric and magnetic field component time histories from the receiver in the model of a metal cylinder buried in a dielectric half-space.
@@ -167,7 +167,7 @@ You can now view an image of the B-scan using the command:
 
 .. _cylinder_Bscan_results:
 
-.. figure:: images/cylinder_Bscan_results.png
+.. figure:: ../../images_shared/cylinder_Bscan_results.png
     :width: 600px
 
     B-scan of model of a metal cylinder buried in a dielectric half-space.

docs/source/gprmodelling.rst

@@ -29,7 +29,7 @@ temporal :math:`\Delta t` steps play a very significant role -- since the smalle
 
 .. _yeecell3D:
 
-.. figure:: images/yeecell3d.png
+.. figure:: ../../images_shared/yeecell3d.png
     :width: 500px
 
     Single FDTD Yee cell showing electric (red) and magnetic (green) field components.
@@ -40,7 +40,7 @@ gprMax is fundamentally based on solving Maxwell's equations in 3D using the FDT
 
 .. _yeecell2DTMz:
 
-.. figure:: images/yeecell2dTMz.png
+.. figure:: ../../images_shared/yeecell2dTMz.png
     :width: 500px
 
     Single FDTD Yee cell showing electric (red), magnetic (green), and zeroed out (grey) field components for 2D transverse magnetic (TM) z-direction mode.
@@ -80,7 +80,7 @@ A right-handed Cartesian coordinate system is used with the origin of space coor
 
 .. _coord3d:
 
-.. figure:: images/coord3d.png
+.. figure:: ../../images_shared/coord3d.png
     :width: 500px
 
     gprMax coordinate system and conventions.
@@ -122,7 +122,7 @@ One of the most challenging issues in modelling *open boundary* problems, such a
 
 .. _abcs:
 
-.. figure:: images/abcs.png
+.. figure:: ../../images_shared/abcs.png
     :width: 600px
 
     GPR forward problem showing computational domain bounded by Absorbing Boundary Conditions (ABCs)

docs/source/include_readme.rst

@@ -1 +0,0 @@
-.. include:: ../../README.rst

docs/source/output.rst

@@ -141,7 +141,7 @@ The ``#geometry_view:`` command produces either ImageData (.vti) for a per-cell
 
 .. _pv_toolbar:
 
-.. figure:: images/paraview_toolbar.png
+.. figure:: ../../images_shared/paraview_toolbar.png
 
     Paraview toolbar showing ``gprMax_info`` macro button.
 
@@ -152,7 +152,7 @@ The ``#geometry_view:`` command produces either ImageData (.vti) for a per-cell
 
 .. _pv_pipeline:
 
-.. figure:: images/paraview_pipeline.png
+.. figure:: ../../images_shared/paraview_pipeline.png
     :width: 350 px
 
     Paraview Pipeline Browser showing list of materials in an example model.

docs/source/plotting.rst

@@ -118,7 +118,7 @@ A Gaussian waveform.
 
 where :math:`\zeta = 2\pi^2f^2`, :math:`\chi=\frac{1}{f}` and :math:`f` is the frequency.
 
-.. figure:: images/gaussian.png
+.. figure:: ../../images_shared/gaussian.png
 
     Example of the ``gaussian`` waveform - time domain and power spectrum.
 
@@ -132,7 +132,7 @@ First derivative of a Gaussian waveform.
 
 where :math:`\zeta = 2\pi^2f^2`, :math:`\chi=\frac{1}{f}` and :math:`f` is the frequency.
 
-.. figure:: images/gaussiandot.png
+.. figure:: ../../images_shared/gaussiandot.png
 
     Example of the ``gaussiandot`` waveform - time domain and power spectrum.
 
@@ -146,7 +146,7 @@ Normalised first derivative of a Gaussian waveform.
 
 where :math:`\zeta = 2\pi^2f^2`, :math:`\chi=\frac{1}{f}` and :math:`f` is the frequency.
 
-.. figure:: images/gaussiandotnorm.png
+.. figure:: ../../images_shared/gaussiandotnorm.png
 
     Example of the ``gaussiandotnorm`` waveform - time domain and power spectrum.
 
@@ -160,7 +160,7 @@ Second derivative of a Gaussian waveform.
 
 where :math:`\zeta = \pi^2f^2`, :math:`\chi=\frac{\sqrt{2}}{f}` and :math:`f` is the frequency.
 
-.. figure:: images/gaussiandotdot.png
+.. figure:: ../../images_shared/gaussiandotdot.png
 
     Example of the ``gaussiandotdot`` waveform - time domain and power spectrum.
 
@@ -174,7 +174,7 @@ Normalised second derivative of a Gaussian waveform.
 
 where :math:`\zeta = \pi^2f^2`, :math:`\chi=\frac{\sqrt{2}}{f}` and :math:`f` is the frequency.
 
-.. figure:: images/gaussiandotdotnorm.png
+.. figure:: ../../images_shared/gaussiandotdotnorm.png
 
     Example of the ``gaussiandotdotnorm`` waveform - time domain and power spectrum.
 
@@ -188,7 +188,7 @@ A Ricker (or Mexican Hat) waveform which is the negative, normalised second deri
 
 where :math:`\zeta = \pi^2f^2`, :math:`\chi=\frac{\sqrt{2}}{f}` and :math:`f` is the frequency.
 
-.. figure:: images/ricker.png
+.. figure:: ../../images_shared/ricker.png
 
     Example of the ``ricker`` waveform - time domain and power spectrum.
 
@@ -212,7 +212,7 @@ and
 
 :math:`f` is the frequency
 
-.. figure:: images/sine.png
+.. figure:: ../../images_shared/sine.png
 
     Example of the ``sine`` waveform - time domain and power spectrum.
 
@@ -236,6 +236,6 @@ and
 
 where :math:`R_c` is set to :math:`0.25` and :math:`f` is the frequency.
 
-.. figure:: images/contsine.png
+.. figure:: ../../images_shared/contsine.png
 
     Example of the ``contsine`` waveform - time domain and power spectrum.

user_libs/AntennaPatterns/README.rst

@@ -48,7 +48,7 @@ How to use the package
     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/antenna_like_GSSI_1500_patterns_E_Er5.png
+.. figure:: ../../images_shared/antenna_like_GSSI_1500_patterns_E_Er5.png
     :width: 600 px
 
     Example of the E-plane pattern from a simulation containing an antenna model similar to a GSSI 1.5 GHz antenna over a homogeneous, lossless half-space with a relative permittivity of five.

user_libs/AustinManWoman/README.rst

@@ -17,7 +17,7 @@ Information
 
 `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>`_.
 
-.. figure:: images/AustinMan_head.png
+.. figure:: ../../images_shared/AustinMan_head.png
     :width: 600 px
 
     FDTD geometry mesh showing the head of the AustinMan model (2x2x2mm :math:`^3`).
@@ -76,7 +76,7 @@ To insert a 2x2x2mm :math:`^3` AustinMan with the lower left corner 40mm from th
 
 For further information on the ``#geometry_objects_read`` see the section on object contruction commands in the :ref:`Input commands section <commands>`.
 
-.. figure:: images/AustinMan.png
+.. figure:: ../../images_shared/AustinMan.png
     :width: 300 px
 
     FDTD geometry mesh showing the AustinMan body model (2x2x2mm :math:`^3`).

user_libs/DebyeFit/README.rst

@@ -36,7 +36,7 @@ where :math:`\epsilon(\omega)` is frequency dependent dielectric permittivity, :
 
 To fit the data to a multi-Debye expansion, you can choose between Havriliak-Negami, Jonscher, or Complex Refractive Index Mixing (CRIM) models, as well as arbitrary dielectric data derived experimentally or calculated using a different function.
 
-.. figure:: images/epsilon.png
+.. figure:: ../../images_shared/epsilon.png
     :width: 600 px
 
     Real and imaginary parts of frequency-dependent permittivity

user_libs/GPRAntennasModels/README.rst

@@ -54,17 +54,17 @@ To include an antenna model similar to a GSSI 1.5 GHz antenna at a location 0.12
     antenna_like_GSSI_1500(0.125, 0.094, 0.100, resolution=0.002)
     #end_python:
 
-.. figure:: images/antenna_like_GSSI_1500.png
+.. figure:: ../../images_shared/antenna_like_GSSI_1500.png
     :width: 600 px
 
     FDTD geometry mesh showing an antenna model similar to a GSSI 1.5 GHz antenna (skid removed for illustrative purposes).
 
-.. figure:: images/antenna_like_GSSI_400.png
+.. figure:: ../../images_shared/antenna_like_GSSI_400.png
     :width: 600 px
 
     FDTD geometry mesh showing an antenna model similar to a GSSI 400 MHz antenna (skid removed for illustrative purposes).
 
-.. figure:: images/antenna_like_MALA_1200.png
+.. figure:: ../../images_shared/antenna_like_MALA_1200.png
     :width: 600 px
 
     FDTD geometry mesh showing an antenna model similar to a MALA 1.2GHz antenna (skid removed for illustrative purposes).

user_libs/LandmineModels/README.rst

@@ -76,12 +76,12 @@ The input file for inserting the PMN landmine, with the lower left corner 10mm f
 
 For further information on the ``#geometry_objects_read`` see the section on object contruction commands in the :ref:`Input commands section <commands>`.
 
-.. figure:: images/PMA.png
+.. figure:: ../../images_shared/PMA.png
     :width: 600 px
 
     FDTD geometry mesh showing the PMA-1 landmine model.
 
-.. figure:: images/PMN.png
+.. figure:: ../../images_shared/PMN.png
     :width: 600 px
 
     FDTD geometry mesh showing the PMN landmine model.

user_libs/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: user_libs/Materials/eccosorb.txt
     #box: 0 0 0 0.5 0.5 0.5 eccosorb_ls22
 
 Eccosorb
@@ -29,42 +29,42 @@ Eccosorb
 
 `Eccosorb <http://www.eccosorb.eu>`_ are electromagnetic absorber materials manufactured by `Laird NV <http://www.eccosorb.eu>`_ (formerly Emerson & Cuming Microwave Products NV). Currently models for some of the LS series (14, 16, 18, 20, 22, 26, 28, and 30) are included in this library. The models were created by fitting a 3-pole Debye model to the real and imaginary parts of the relative permittivity taken from the `manufacturers datasheet <http://www.eccosorb.com/Collateral/Documents/English-US/Electrical%20Parameters/ls%20parameters.pdf>`_. The following figures show the fitting.
 
-.. figure:: images/eccosorb_ls14.png
+.. figure:: ../../images_shared/eccosorb_ls14.png
     :width: 600 px
 
     3-pole Debye fit for Eccosorb LS14 absorber (HN indicates data from manufacturer datasheet)
 
-.. figure:: images/eccosorb_ls16.png
+.. figure:: ../../images_shared/eccosorb_ls16.png
     :width: 600 px
 
     3-pole Debye fit for Eccosorb LS16 absorber (HN indicates data from manufacturer datasheet)
 
-.. figure:: images/eccosorb_ls18.png
+.. figure:: ../../images_shared/eccosorb_ls18.png
     :width: 600 px
 
     3-pole Debye fit for Eccosorb LS18 absorber (HN indicates data from manufacturer datasheet)
 
-.. figure:: images/eccosorb_ls20.png
+.. figure:: ../../images_shared/eccosorb_ls20.png
     :width: 600 px
 
     3-pole Debye fit for Eccosorb LS20 absorber (HN indicates data from manufacturer datasheet)
 
-.. figure:: images/eccosorb_ls22.png
+.. figure:: ../../images_shared/eccosorb_ls22.png
     :width: 600 px
 
     3-pole Debye fit for Eccosorb LS22 absorber (HN indicates data from manufacturer datasheet)
 
-.. figure:: images/eccosorb_ls26.png
+.. figure:: ../../images_shared/eccosorb_ls26.png
     :width: 600 px
 
     3-pole Debye fit for Eccosorb LS26 absorber (HN indicates data from manufacturer datasheet)
 
-.. figure:: images/eccosorb_ls28.png
+.. figure:: ../../images_shared/eccosorb_ls28.png
     :width: 600 px
 
     3-pole Debye fit for Eccosorb LS28 absorber (HN indicates data from manufacturer datasheet)
 
-.. figure:: images/eccosorb_ls30.png
+.. figure:: ../../images_shared/eccosorb_ls30.png
     :width: 600 px
 
     3-pole Debye fit for Eccosorb LS30 absorber (HN indicates data from manufacturer datasheet)

user_libs/stltovoxel/README.rst

@@ -49,22 +49,22 @@ Since the number of voxels are 108 x 88 108 and the spatial discretisation chose
 
 The following is an example of a ``materials.txt`` file that can be used with the generated geometry file (HDF5 format) when importing into gprMax. Since ``-matindex`` is set to 2 the material with name ``hdpe``, i.e. a plastic, will be used.
 
-.. literalinclude:: ../examples/materials.txt
+.. literalinclude:: examples/materials.txt
     :language: none
     :linenos:
 
 The following Python script (using the gprMax API) can be used to import the generated geometry file ``Stanford_Bunny.h5`` and materials file ``materials.txt`` into a gprMax model:
 
-.. literalinclude:: ../examples/bunny.py
+.. literalinclude:: examples/bunny.py
     :language: python
     :linenos:
 
-.. figure:: images/stanford_bunny_stl.png
+.. figure:: ../../images_shared/stanford_bunny_stl.png
     :width: 600 px
 
     Image of the Stanford bunny STL file
 
-.. figure:: images/stanford_bunny.png
+.. figure:: ../../images_shared/stanford_bunny.png
     :width: 600 px
 
     FDTD geometry mesh showing the Stanford bunny