autopep8 code cleanups.

2025-08-03 19:26:50 +08:00 · 2017-02-22 10:37:30 +00:00
--- a/docs/source/conf.py
+++ b/docs/source/conf.py
@@ -25,7 +25,7 @@ sys.path.insert(0, os.path.abspath('../..'))
 # -- General configuration ------------------------------------------------

 # If your documentation needs a minimal Sphinx version, state it here.
-#needs_sphinx = '1.0'
+# needs_sphinx = '1.0'

 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
@@ -35,7 +35,7 @@ extensions = [
 ]

 # autodoc mock imports
-#autodoc_mock_imports = ['h5py', 'matplotlib', 'pyfiglet', 'cython', 'psutil']
+# autodoc_mock_imports = ['h5py', 'matplotlib', 'pyfiglet', 'cython', 'psutil']

 # Options for autodoc
 autodoc_default_flags = ['members']
@@ -57,7 +57,7 @@ templates_path = ['_templates']
 source_suffix = '.rst'

 # The encoding of source files.
-#source_encoding = 'utf-8-sig'
+# source_encoding = 'utf-8-sig'

 # The master toctree document.
 master_doc = 'index'
@@ -87,9 +87,9 @@ language = None

 # There are two options for replacing |today|: either, you set today to some
 # non-false value, then it is used:
-#today = ''
+# today = ''
 # Else, today_fmt is used as the format for a strftime call.
-#today_fmt = '%B %d, %Y'
+# today_fmt = '%B %d, %Y'

 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
@@ -97,27 +97,27 @@ exclude_patterns = ['_build']

 # The reST default role (used for this markup: `text`) to use for all
 # documents.
-#default_role = None
+# default_role = None

 # If true, '()' will be appended to :func: etc. cross-reference text.
-#add_function_parentheses = True
+# add_function_parentheses = True

 # If true, the current module name will be prepended to all description
 # unit titles (such as .. function::).
-#add_module_names = True
+# add_module_names = True

 # If true, sectionauthor and moduleauthor directives will be shown in the
 # output. They are ignored by default.
-#show_authors = False
+# show_authors = False

 # The name of the Pygments (syntax highlighting) style to use.
 pygments_style = 'sphinx'

 # A list of ignored prefixes for module index sorting.
-#modindex_common_prefix = []
+# modindex_common_prefix = []

 # If true, keep warnings as "system message" paragraphs in the built documents.
-#keep_warnings = False
+# keep_warnings = False

 # If true, `todo` and `todoList` produce output, else they produce nothing.
 todo_include_todos = False
@@ -132,26 +132,26 @@ html_theme = 'sphinx_rtd_theme'
 # Theme options are theme-specific and customize the look and feel of a theme
 # further.  For a list of options available for each theme, see the
 # documentation.
-#html_theme_options = {}
+# html_theme_options = {}

 # Add any paths that contain custom themes here, relative to this directory.
-#html_theme_path = []
+# html_theme_path = []

 # The name for this set of Sphinx documents.  If None, it defaults to
 # "<project> v<release> documentation".
 html_title = 'gprMax User Guide'

 # A shorter title for the navigation bar.  Default is the same as html_title.
-#html_short_title = None
+# html_short_title = None

 # 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/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
 # pixels large.
-#html_favicon = None
+# html_favicon = None

 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
@@ -162,7 +162,7 @@ html_style = 'css/my_theme.css'
 # Add any extra paths that contain custom files (such as robots.txt or
 # .htaccess) here, relative to this directory. These files are copied
 # directly to the root of the documentation.
-#html_extra_path = []
+# html_extra_path = []

 # If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
 # using the given strftime format.
@@ -170,54 +170,54 @@ html_last_updated_fmt = '%b %d, %Y'

 # If true, SmartyPants will be used to convert quotes and dashes to
 # typographically correct entities.
-#html_use_smartypants = True
+# html_use_smartypants = True

 # Custom sidebar templates, maps document names to template names.
-#html_sidebars = {}
+# html_sidebars = {}

 # Additional templates that should be rendered to pages, maps page names to
 # template names.
-#html_additional_pages = {}
+# html_additional_pages = {}

 # If false, no module index is generated.
-#html_domain_indices = True
+# html_domain_indices = True

 # If false, no index is generated.
-#html_use_index = True
+# html_use_index = True

 # If true, the index is split into individual pages for each letter.
-#html_split_index = False
+# html_split_index = False

 # If true, links to the reST sources are added to the pages.
 html_show_sourcelink = False

 # If true, "Created using Sphinx" is shown in the HTML footer. Default is True.
-#html_show_sphinx = True
+# html_show_sphinx = True

 # If true, "(C) Copyright ..." is shown in the HTML footer. Default is True.
-#html_show_copyright = True
+# html_show_copyright = True

 # If true, an OpenSearch description file will be output, and all pages will
 # contain a <link> tag referring to it.  The value of this option must be the
 # base URL from which the finished HTML is served.
-#html_use_opensearch = ''
+# html_use_opensearch = ''

 # This is the file name suffix for HTML files (e.g. ".xhtml").
-#html_file_suffix = None
+# html_file_suffix = None

 # Language to be used for generating the HTML full-text search index.
 # Sphinx supports the following languages:
 #   'da', 'de', 'en', 'es', 'fi', 'fr', 'h', 'it', 'ja'
 #   'nl', 'no', 'pt', 'ro', 'r', 'sv', 'tr'
-#html_search_language = 'en'
+# html_search_language = 'en'

 # A dictionary with options for the search language support, empty by default.
 # Now only 'ja' uses this config value
-#html_search_options = {'type': 'default'}
+# html_search_options = {'type': 'default'}

 # The name of a javascript file (relative to the configuration directory) that
 # implements a search results scorer. If empty, the default will be used.
-#html_search_scorer = 'scorer.js'
+# html_search_scorer = 'scorer.js'

 # Output file base name for HTML help builder.
 htmlhelp_basename = 'gprMaxdoc'
@@ -229,13 +229,13 @@ latex_elements = {
    'papersize': 'a4paper',

    # The font size ('10pt', '11pt' or '12pt').
-    #'pointsize': '10pt',
+    # 'pointsize': '10pt',

    # Additional stuff for the LaTeX preamble.
-    #'preamble': '',
+    # 'preamble': '',

    # Latex figure (float) alignment
-    #'figure_align': 'htbp',
+    # 'figure_align': 'htbp',
 }

 # Grouping the document tree into LaTeX files. List of tuples
@@ -252,19 +252,19 @@ latex_logo = 'images/gprMax_logo.png'

 # For "manual" documents, if this is true, then toplevel headings are parts,
 # not chapters.
-#latex_use_parts = False
+# latex_use_parts = False

 # If true, show page references after internal links.
-#latex_show_pagerefs = False
+# latex_show_pagerefs = False

 # If true, show URL addresses after external links.
 latex_show_urls = 'inline'

 # Documents to append as an appendix to all manuals.
-#latex_appendices = []
+# latex_appendices = []

 # If false, no module index is generated.
-#latex_domain_indices = True
+# latex_domain_indices = True


 # -- Options for manual page output ---------------------------------------
@@ -277,7 +277,7 @@ man_pages = [
 ]

 # If true, show URL addresses after external links.
-#man_show_urls = False
+# man_show_urls = False


 # -- Options for Texinfo output -------------------------------------------
@@ -292,16 +292,16 @@ texinfo_documents = [
 ]

 # Documents to append as an appendix to all manuals.
-#texinfo_appendices = []
+# texinfo_appendices = []

 # If false, no module index is generated.
-#texinfo_domain_indices = True
+# texinfo_domain_indices = True

 # How to display URL addresses: 'footnote', 'no', or 'inline'.
-#texinfo_show_urls = 'footnote'
+# texinfo_show_urls = 'footnote'

 # If true, do not generate a @detailmenu in the "Top" node's menu.
-#texinfo_no_detailmenu = False
+# texinfo_no_detailmenu = False


 # -- Options for Epub output ----------------------------------------------
@@ -319,11 +319,11 @@ epub_basename = 'gprMax User Guide'
 # for small screen space, using the same theme for HTML and epub output is
 # usually not wise. This defaults to 'epub', a theme designed to save visual
 # space.
-#epub_theme = 'epub'
+# epub_theme = 'epub'

 # The language of the text. It defaults to the language option
 # or 'en' if the language is not set.
-#epub_language = ''
+# epub_language = ''

 # The scheme of the identifier. Typical schemes are ISBN or URL.
 epub_scheme = 'URL'
@@ -333,42 +333,42 @@ epub_scheme = 'URL'
 epub_identifier = 'www.gprmax.com'

 # A unique identification for the text.
-#epub_uid = ''
+# epub_uid = ''

 # A tuple containing the cover image and cover page html template filenames.
-#epub_cover = ()
+# epub_cover = ()

 # A sequence of (type, uri, title) tuples for the guide element of content.opf.
-#epub_guide = ()
+# epub_guide = ()

 # HTML files that should be inserted before the pages created by sphinx.
 # The format is a list of tuples containing the path and title.
-#epub_pre_files = []
+# epub_pre_files = []

 # HTML files shat should be inserted after the pages created by sphinx.
 # The format is a list of tuples containing the path and title.
-#epub_post_files = []
+# epub_post_files = []

 # A list of files that should not be packed into the epub file.
 epub_exclude_files = ['search.html']

 # The depth of the table of contents in toc.ncx.
-#epub_tocdepth = 3
+# epub_tocdepth = 3

 # Allow duplicate toc entries.
-#epub_tocdup = True
+# epub_tocdup = True

 # Choose between 'default' and 'includehidden'.
-#epub_tocscope = 'default'
+# epub_tocscope = 'default'

 # Fix unsupported image types using the Pillow.
-#epub_fix_images = False
+# epub_fix_images = False

 # Scale large images.
-#epub_max_image_width = 0
+# epub_max_image_width = 0

 # How to display URL addresses: 'footnote', 'no', or 'inline'.
-#epub_show_urls = 'inline'
+# epub_show_urls = 'inline'

 # If false, no index is generated.
-#epub_use_index = True
+# epub_use_index = True
--- a/tests/benchmarking/plot_benchmark.py
+++ b/tests/benchmarking/plot_benchmark.py
@@ -67,10 +67,10 @@ if args.otherresults is not None:
    for i, result in enumerate(otherresults):
        ax.plot(result['threads'], result['benchtimes'], color=colors[1], marker='.', ms=10, lw=2, ls=lines[i], label=otherplotlabels[i] + ' (v' + version + ')')

-#ax.plot(results['threads'], results['bench1'], color=colors[1], marker='.', ms=10, lw=2, label='bench_100x100x100.in (v3.0.0b21)')
-#ax.plot(results['threads'], results['bench1c'], color=colors[0], marker='.', ms=10, lw=2, label='bench_100x100x100.in (v2)')
-#ax.plot(results['threads'], results['bench2'], color=colors[1], marker='.', ms=10, lw=2, ls='--', label='bench_150x150x150.in (v3.0.0b21)')
-#ax.plot(results['threads'], results['bench2c'], color=colors[0], marker='.', ms=10, lw=2, ls='--', label='bench_150x150x150.in (v2)')
+# ax.plot(results['threads'], results['bench1'], color=colors[1], marker='.', ms=10, lw=2, label='bench_100x100x100.in (v3.0.0b21)')
+# ax.plot(results['threads'], results['bench1c'], color=colors[0], marker='.', ms=10, lw=2, label='bench_100x100x100.in (v2)')
+# ax.plot(results['threads'], results['bench2'], color=colors[1], marker='.', ms=10, lw=2, ls='--', label='bench_150x150x150.in (v3.0.0b21)')
+# ax.plot(results['threads'], results['bench2c'], color=colors[0], marker='.', ms=10, lw=2, ls='--', label='bench_150x150x150.in (v2)')

 ax.set_xlabel('Number of threads')
 ax.set_ylabel('Time [s]')
@@ -91,10 +91,10 @@ if args.otherresults is not None:
    for i, result in enumerate(otherresults):
        ax.plot(result['threads'], result['benchtimes'][-1] / result['benchtimes'], color=colors[1], marker='.', ms=10, lw=2, ls=lines[i], label=otherplotlabels[i] + ' (v' + version + ')')

-#ax.plot(results['threads'], results['bench1'][0] / results['bench1'], color=colors[1], marker='.', ms=10, lw=2, label='bench_100x100x100.in (v3.0.0b21)')
-#ax.plot(results['threads'], results['bench1c'][1] / results['bench1c'], color=colors[0], marker='.', ms=10, lw=2, label='bench_100x100x100.in (v2)')
-#ax.plot(results['threads'], results['bench2'][0] / results['bench2'], color=colors[1], marker='.', ms=10, lw=2, ls='--', label='bench_150x150x150.in (v3.0.0b21)')
-#ax.plot(results['threads'], results['bench2c'][1] / results['bench2c'], color=colors[0], marker='.', ms=10, lw=2, ls='--', label='bench_150x150x150.in (v2)')
+# ax.plot(results['threads'], results['bench1'][0] / results['bench1'], color=colors[1], marker='.', ms=10, lw=2, label='bench_100x100x100.in (v3.0.0b21)')
+# ax.plot(results['threads'], results['bench1c'][1] / results['bench1c'], color=colors[0], marker='.', ms=10, lw=2, label='bench_100x100x100.in (v2)')
+# ax.plot(results['threads'], results['bench2'][0] / results['bench2'], color=colors[1], marker='.', ms=10, lw=2, ls='--', label='bench_150x150x150.in (v3.0.0b21)')
+# ax.plot(results['threads'], results['bench2c'][1] / results['bench2c'], color=colors[0], marker='.', ms=10, lw=2, ls='--', label='bench_150x150x150.in (v2)')

 ax.set_xlabel('Number of threads')
 ax.set_ylabel('Speed-up factor')
--- a/tests/test_experimental.py
+++ b/tests/test_experimental.py
@@ -84,7 +84,7 @@ ax.grid()

 # Save a PDF/PNG of the figure
 savename = os.path.abspath(os.path.dirname(args.modelfile)) + os.sep + os.path.splitext(os.path.split(args.modelfile)[1])[0] + '_vs_' + os.path.splitext(os.path.split(args.realfile)[1])[0]
-#fig.savefig(savename + '.pdf', dpi=None, format='pdf', bbox_inches='tight', pad_inches=0.1)
+# fig.savefig(savename + '.pdf', dpi=None, format='pdf', bbox_inches='tight', pad_inches=0.1)
 # fig.savefig((savename + '.png', dpi=150, format='png', bbox_inches='tight', pad_inches=0.1)

 plt.show()
--- a/tests/test_input_cmd_funcs.py
+++ b/tests/test_input_cmd_funcs.py
@@ -47,11 +47,6 @@ class My_input_cmd_funcs_test(unittest.TestCase):
            rx(2, 1, 0, 'id', ['Ex', 'Ez'])
        self.assert_output(out, '#rx: 2 1 0 id Ex Ez')

-    def test_rx4(self):
-        with captured_output() as (out, err):
-            rx(2, 1, 0, 'id', ['Ex', 'Ez'])
-        self.assert_output(out, '#rx: 2 1 0 id Ex Ez')
-
    def test_rx_rotate_exception(self):
        with self.assertRaises(ValueError):
            rx(2, 1, 0, 'id', ['Ex', 'Ez'], polarisation='x', rotate90origin=(1, 1))  # no dxdy given
--- a/tests/test_models.py
+++ b/tests/test_models.py
@@ -41,17 +41,17 @@ from tests.analytical_solutions import hertzian_dipole_fs

 basepath = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'models_')
 basepath += 'basic'
-#basepath += 'advanced'
+# basepath += 'advanced'

 # List of available basic test models
 testmodels = ['hertzian_dipole_fs_analytical', '2D_ExHyHz', '2D_EyHxHz', '2D_EzHxHy', 'cylinder_Ascan_2D', 'hertzian_dipole_fs', 'hertzian_dipole_hs', 'hertzian_dipole_dispersive', 'magnetic_dipole_fs']

 # List of available advanced test models
-#testmodels = ['antenna_GSSI_1500_fs', 'antenna_MALA_1200_fs']
+# testmodels = ['antenna_GSSI_1500_fs', 'antenna_MALA_1200_fs']

 # Select a specific model if desired
-#testmodels = [testmodels[0], testmodels[5], testmodels[7]]
-#testmodels = [testmodels[5]]
+# testmodels = [testmodels[0], testmodels[5], testmodels[7]]
+# testmodels = [testmodels[5]]
 testresults = dict.fromkeys(testmodels)
 path = '/rxs/rx1/'

@@ -138,9 +138,9 @@ for i, model in enumerate(testmodels):
    datadiffs = np.zeros(datatest.shape, dtype=np.float64)
    for i in range(len(outputstest)):
        max = np.amax(np.abs(dataref[:, i]))
-        datadiffs[:, i] = np.divide(np.abs(dataref[:, i] - datatest[:, i]), max, out=np.zeros_like(dataref[:, i]), where=max!=0) # Replace any division by zero with zero
+        datadiffs[:, i] = np.divide(np.abs(dataref[:, i] - datatest[:, i]), max, out=np.zeros_like(dataref[:, i]), where=max != 0)  # Replace any division by zero with zero
        with np.errstate(divide='ignore'):
-            datadiffs[:, i] = 20 * np.log10(datadiffs[:, i]) # Ignore any zero division in log10
+            datadiffs[:, i] = 20 * np.log10(datadiffs[:, i])  # Ignore any zero division in log10

    # Store max difference
    maxdiff = np.amax(np.amax(datadiffs))
@@ -184,8 +184,8 @@ for i, model in enumerate(testmodels):

    # Save a PDF/PNG of the figure
    savename = os.path.join(basepath, model + os.path.sep + model)
-    #fig1.savefig(savename + '.pdf', dpi=None, format='pdf', bbox_inches='tight', pad_inches=0.1)
-    #fig2.savefig(savename + '_diffs.pdf', dpi=None, format='pdf', bbox_inches='tight', pad_inches=0.1)
+    # fig1.savefig(savename + '.pdf', dpi=None, format='pdf', bbox_inches='tight', pad_inches=0.1)
+    # fig2.savefig(savename + '_diffs.pdf', dpi=None, format='pdf', bbox_inches='tight', pad_inches=0.1)
    fig1.savefig(savename + '.png', dpi=150, format='png', bbox_inches='tight', pad_inches=0.1)
    fig2.savefig(savename + '_diffs.png', dpi=150, format='png', bbox_inches='tight', pad_inches=0.1)

--- a/macros/gprMax_info.py
+++ b/macros/gprMax_info.py
@@ -111,7 +111,8 @@ if rxs:
                thresholddisplay = Show(threshold, renderview)
                thresholddisplay.ColorArrayName = 'Receivers'

-#renderview.CameraParallelProjection = 1
+# renderview.CameraParallelProjection = 1
 RenderAllViews()
+
 # Show color bar/color legend
-#thresholdDisplay.SetScalarBarVisibility(renderview, False)
+# thresholdDisplay.SetScalarBarVisibility(renderview, False)
--- a/tools/plot_Ascan.py
+++ b/tools/plot_Ascan.py
@@ -93,7 +93,7 @@ def mpl_plot(filename, outputs=Rx.defaultoutputs, fft=False):
                # Set plotting range to -60dB from maximum power
                pltrange = np.where((np.amax(power[1::]) - power[1::]) > 60)[0][0] + 1
                # To a maximum frequency
-                #pltrange = np.where(freqs > 2e9)[0][0]
+                # pltrange = np.where(freqs > 2e9)[0][0]
                pltrange = np.s_[0:pltrange]

                # Plot time history of output component
@@ -135,7 +135,7 @@ def mpl_plot(filename, outputs=Rx.defaultoutputs, fft=False):
                fig, ax = plt.subplots(subplot_kw=dict(xlabel='Time [s]', ylabel=outputtext + ' field strength [V/m]'), num='rx' + str(rx), figsize=(20, 10), facecolor='w', edgecolor='w')
                line = ax.plot(time, outputdata, 'r', lw=2, label=outputtext)
                ax.set_xlim([0, np.amax(time)])
-                #ax.set_ylim([-15, 20])
+                # ax.set_ylim([-15, 20])
                ax.grid()

                if 'H' in output:
@@ -152,7 +152,7 @@ def mpl_plot(filename, outputs=Rx.defaultoutputs, fft=False):
                gs = gridspec.GridSpec(3, 3, hspace=0.3, wspace=0.3)
            else:
                gs = gridspec.GridSpec(3, 2, hspace=0.3, wspace=0.3)
-            
+
            for output in outputs:
                # Check for polarity of output and if requested output is in file
                if output[-1] == 'm':
@@ -173,51 +173,51 @@ def mpl_plot(filename, outputs=Rx.defaultoutputs, fft=False):
                    ax = plt.subplot(gs[0, 0])
                    ax.plot(time, outputdata, 'r', lw=2, label=outputtext)
                    ax.set_ylabel(outputtext + ', field strength [V/m]')
-                #ax.set_ylim([-15, 20])
+                # ax.set_ylim([-15, 20])
                elif output == 'Ey':
                    ax = plt.subplot(gs[1, 0])
                    ax.plot(time, outputdata, 'r', lw=2, label=outputtext)
                    ax.set_ylabel(outputtext + ', field strength [V/m]')
-                #ax.set_ylim([-15, 20])
+                # ax.set_ylim([-15, 20])
                elif output == 'Ez':
                    ax = plt.subplot(gs[2, 0])
                    ax.plot(time, outputdata, 'r', lw=2, label=outputtext)
                    ax.set_ylabel(outputtext + ', field strength [V/m]')
-                #ax.set_ylim([-15, 20])
+                # ax.set_ylim([-15, 20])
                elif output == 'Hx':
                    ax = plt.subplot(gs[0, 1])
                    ax.plot(time, outputdata, 'g', lw=2, label=outputtext)
                    ax.set_ylabel(outputtext + ', field strength [A/m]')
-                #ax.set_ylim([-0.03, 0.03])
+                # ax.set_ylim([-0.03, 0.03])
                elif output == 'Hy':
                    ax = plt.subplot(gs[1, 1])
                    ax.plot(time, outputdata, 'g', lw=2, label=outputtext)
                    ax.set_ylabel(outputtext + ', field strength [A/m]')
-                #ax.set_ylim([-0.03, 0.03])
+                # ax.set_ylim([-0.03, 0.03])
                elif output == 'Hz':
                    ax = plt.subplot(gs[2, 1])
                    ax.plot(time, outputdata, 'g', lw=2, label=outputtext)
                    ax.set_ylabel(outputtext + ', field strength [A/m]')
-                #ax.set_ylim([-0.03, 0.03])
+                # ax.set_ylim([-0.03, 0.03])
                elif output == 'Ix':
                    ax = plt.subplot(gs[0, 2])
-                    ax.plot(time, outputdata,'b', lw=2, label=outputtext)
+                    ax.plot(time, outputdata, 'b', lw=2, label=outputtext)
                    ax.set_ylabel(outputtext + ', current [A]')
                elif output == 'Iy':
                    ax = plt.subplot(gs[1, 2])
-                    ax.plot(time, outputdata,'b', lw=2, label=outputtext)
+                    ax.plot(time, outputdata, 'b', lw=2, label=outputtext)
                    ax.set_ylabel(outputtext + ', current [A]')
                elif output == 'Iz':
                    ax = plt.subplot(gs[2, 2])
-                    ax.plot(time, outputdata,'b', lw=2, label=outputtext)
+                    ax.plot(time, outputdata, 'b', lw=2, label=outputtext)
                    ax.set_ylabel(outputtext + ', current [A]')
            for ax in fig.axes:
                ax.set_xlim([0, np.amax(time)])
                ax.grid()

        # Save a PDF/PNG of the figure
-#        fig.savefig(os.path.splitext(os.path.abspath(filename))[0] + '_rx' + str(rx) + '.pdf', dpi=None, format='pdf', bbox_inches='tight', pad_inches=0.1)
-#        fig.savefig(os.path.splitext(os.path.abspath(filename))[0] + '_rx' + str(rx) + '.png', dpi=150, format='png', bbox_inches='tight', pad_inches=0.1)
+        # fig.savefig(os.path.splitext(os.path.abspath(filename))[0] + '_rx' + str(rx) + '.pdf', dpi=None, format='pdf', bbox_inches='tight', pad_inches=0.1)
+        # fig.savefig(os.path.splitext(os.path.abspath(filename))[0] + '_rx' + str(rx) + '.png', dpi=150, format='png', bbox_inches='tight', pad_inches=0.1)

    return plt

--- a/tools/plot_Bscan.py
+++ b/tools/plot_Bscan.py
@@ -93,8 +93,8 @@ def mpl_plot(outputdata, dt, rxnumber, rxcomponent):
        cb.set_label('Current [A]')

    # Save a PDF/PNG of the figure
-    #fig.savefig('Bscan' + str(rxnumber) + '.pdf', dpi=None, format='pdf', bbox_inches='tight', pad_inches=0.1)
-    #fig.savefig('Bscan' + str(rxnumber) + '.png', dpi=150, format='png', bbox_inches='tight', pad_inches=0.1)
+    # fig.savefig('Bscan' + str(rxnumber) + '.pdf', dpi=None, format='pdf', bbox_inches='tight', pad_inches=0.1)
+    # fig.savefig('Bscan' + str(rxnumber) + '.png', dpi=150, format='png', bbox_inches='tight', pad_inches=0.1)

    return plt

--- a/tools/plot_antenna_params.py
+++ b/tools/plot_antenna_params.py
@@ -155,7 +155,7 @@ def mpl_plot(filename, time, freqs, Vinc, Vincp, Iinc, Iincp, Vref, Vrefp, Iref,
    # To a certain drop from maximum power
    pltrangemax = np.where((np.amax(Vincp[1::]) - Vincp[1::]) > 60)[0][0] + 1
    # To a maximum frequency
-    #pltrangemax = np.where(freqs > 6e9)[0][0]
+    # pltrangemax = np.where(freqs > 6e9)[0][0]
    pltrange = np.s_[pltrangemin:pltrangemax]

    # Print some useful values from s11, and input impedance
@@ -163,8 +163,8 @@ def mpl_plot(filename, time, freqs, Vinc, Vincp, Iinc, Iincp, Vref, Vrefp, Iref,
    print('s11 minimum: {:g} dB at {:g} Hz'.format(np.amin(s11[pltrange]), freqs[s11minfreq + pltrangemin]))
    print('At {:g} Hz...'.format(freqs[s11minfreq + pltrangemin]))
    print('Input impedance: {:.1f}{:+.1f}j Ohms'.format(np.abs(zin[s11minfreq + pltrangemin]), zin[s11minfreq + pltrangemin].imag))
-    #print('Input admittance (mag): {:g} S'.format(np.abs(yin[s11minfreq + pltrangemin])))
-    #print('Input admittance (phase): {:.1f} deg'.format(np.angle(yin[s11minfreq + pltrangemin], deg=True)))
+    # print('Input admittance (mag): {:g} S'.format(np.abs(yin[s11minfreq + pltrangemin])))
+    # print('Input admittance (phase): {:.1f} deg'.format(np.angle(yin[s11minfreq + pltrangemin], deg=True)))

    # Figure 1
    # Plot incident voltage
@@ -254,45 +254,45 @@ def mpl_plot(filename, time, freqs, Vinc, Vincp, Iinc, Iincp, Vref, Vrefp, Iref,
    ax.grid()

    # Plot reflected (reflected) voltage
-    #ax = plt.subplot(gs1[4, 0])
-    #ax.plot(time, Vref, 'r', lw=2, label='Vref')
-    #ax.set_title('Reflected voltage')
-    #ax.set_xlabel('Time [s]')
-    #ax.set_ylabel('Voltage [V]')
-    #ax.set_xlim([0, np.amax(time)])
+    # ax = plt.subplot(gs1[4, 0])
+    # ax.plot(time, Vref, 'r', lw=2, label='Vref')
+    # ax.set_title('Reflected voltage')
+    # ax.set_xlabel('Time [s]')
+    # ax.set_ylabel('Voltage [V]')
+    # ax.set_xlim([0, np.amax(time)])
    # ax.grid()
-    #
+
    # Plot frequency spectra of reflected voltage
-    #ax = plt.subplot(gs1[4, 1])
-    #markerline, stemlines, baseline = ax.stem(freqs[pltrange], Vrefp[pltrange], '-.')
-    #plt.setp(baseline, 'linewidth', 0)
-    #plt.setp(stemlines, 'color', 'r')
-    #plt.setp(markerline, 'markerfacecolor', 'r', 'markeredgecolor', 'r')
-    #ax.plot(freqs[pltrange], Vrefp[pltrange], 'r', lw=2)
-    #ax.set_title('Reflected voltage')
-    #ax.set_xlabel('Frequency [Hz]')
-    #ax.set_ylabel('Power [dB]')
+    # ax = plt.subplot(gs1[4, 1])
+    # markerline, stemlines, baseline = ax.stem(freqs[pltrange], Vrefp[pltrange], '-.')
+    # plt.setp(baseline, 'linewidth', 0)
+    # plt.setp(stemlines, 'color', 'r')
+    # plt.setp(markerline, 'markerfacecolor', 'r', 'markeredgecolor', 'r')
+    # ax.plot(freqs[pltrange], Vrefp[pltrange], 'r', lw=2)
+    # ax.set_title('Reflected voltage')
+    # ax.set_xlabel('Frequency [Hz]')
+    # ax.set_ylabel('Power [dB]')
    # ax.grid()
-    #
+
    # Plot reflected (reflected) current
-    #ax = plt.subplot(gs1[5, 0])
-    #ax.plot(time, Iref, 'b', lw=2, label='Iref')
-    #ax.set_title('Reflected current')
-    #ax.set_xlabel('Time [s]')
-    #ax.set_ylabel('Current [A]')
-    #ax.set_xlim([0, np.amax(time)])
+    # ax = plt.subplot(gs1[5, 0])
+    # ax.plot(time, Iref, 'b', lw=2, label='Iref')
+    # ax.set_title('Reflected current')
+    # ax.set_xlabel('Time [s]')
+    # ax.set_ylabel('Current [A]')
+    # ax.set_xlim([0, np.amax(time)])
    # ax.grid()
-    #
+
    # Plot frequency spectra of reflected current
-    #ax = plt.subplot(gs1[5, 1])
-    #markerline, stemlines, baseline = ax.stem(freqs[pltrange], Irefp[pltrange], '-.')
-    #plt.setp(baseline, 'linewidth', 0)
-    #plt.setp(stemlines, 'color', 'b')
-    #plt.setp(markerline, 'markerfacecolor', 'b', 'markeredgecolor', 'b')
-    #ax.plot(freqs[pltrange], Irefp[pltrange], 'b', lw=2)
-    #ax.set_title('Reflected current')
-    #ax.set_xlabel('Frequency [Hz]')
-    #ax.set_ylabel('Power [dB]')
+    # ax = plt.subplot(gs1[5, 1])
+    # markerline, stemlines, baseline = ax.stem(freqs[pltrange], Irefp[pltrange], '-.')
+    # plt.setp(baseline, 'linewidth', 0)
+    # plt.setp(stemlines, 'color', 'b')
+    # plt.setp(markerline, 'markerfacecolor', 'b', 'markeredgecolor', 'b')
+    # ax.plot(freqs[pltrange], Irefp[pltrange], 'b', lw=2)
+    # ax.set_title('Reflected current')
+    # ax.set_xlabel('Frequency [Hz]')
+    # ax.set_ylabel('Power [dB]')
    # ax.grid()

    # Figure 2
@@ -308,8 +308,8 @@ def mpl_plot(filename, time, freqs, Vinc, Vincp, Iinc, Iincp, Vref, Vrefp, Iref,
    ax.set_title('s11')
    ax.set_xlabel('Frequency [Hz]')
    ax.set_ylabel('Power [dB]')
-    #ax.set_xlim([0, 5e9])
-    #ax.set_ylim([-25, 0])
+    # ax.set_xlim([0, 5e9])
+    # ax.set_ylim([-25, 0])
    ax.grid()

    # Plot frequency spectra of s21
@@ -323,8 +323,8 @@ def mpl_plot(filename, time, freqs, Vinc, Vincp, Iinc, Iincp, Vref, Vrefp, Iref,
        ax.set_title('s21')
        ax.set_xlabel('Frequency [Hz]')
        ax.set_ylabel('Power [dB]')
-        #ax.set_xlim([0.88e9, 1.02e9])
-        #ax.set_ylim([-25, 50])
+        # ax.set_xlim([0.88e9, 1.02e9])
+        # ax.set_ylim([-25, 50])
        ax.grid()

    # Plot input resistance (real part of impedance)
@@ -337,9 +337,9 @@ def mpl_plot(filename, time, freqs, Vinc, Vincp, Iinc, Iincp, Vref, Vrefp, Iref,
    ax.set_title('Input impedance (resistive)')
    ax.set_xlabel('Frequency [Hz]')
    ax.set_ylabel('Resistance [Ohms]')
-    #ax.set_xlim([0.88e9, 1.02e9])
+    # ax.set_xlim([0.88e9, 1.02e9])
    ax.set_ylim(bottom=0)
-    #ax.set_ylim([0, 300])
+    # ax.set_ylim([0, 300])
    ax.grid()

    # Plot input reactance (imaginery part of impedance)
@@ -352,43 +352,43 @@ def mpl_plot(filename, time, freqs, Vinc, Vincp, Iinc, Iincp, Vref, Vrefp, Iref,
    ax.set_title('Input impedance (reactive)')
    ax.set_xlabel('Frequency [Hz]')
    ax.set_ylabel('Reactance [Ohms]')
-    #ax.set_xlim([0.88e9, 1.02e9])
-    #ax.set_ylim([-300, 300])
+    # ax.set_xlim([0.88e9, 1.02e9])
+    # ax.set_ylim([-300, 300])
    ax.grid()

    # Plot input admittance (magnitude)
-    #ax = plt.subplot(gs2[2, 0])
-    #markerline, stemlines, baseline = ax.stem(freqs[pltrange], np.abs(yin[pltrange]), '-.')
-    #plt.setp(baseline, 'linewidth', 0)
-    #plt.setp(stemlines, 'color', 'g')
-    #plt.setp(markerline, 'markerfacecolor', 'g', 'markeredgecolor', 'g')
-    #ax.plot(freqs[pltrange], np.abs(yin[pltrange]), 'g', lw=2)
-    #ax.set_title('Input admittance (magnitude)')
-    #ax.set_xlabel('Frequency [Hz]')
-    #ax.set_ylabel('Admittance [Siemens]')
-    ##ax.set_xlim([0.88e9, 1.02e9])
-    ##ax.set_ylim([0, 0.035])
+    # ax = plt.subplot(gs2[2, 0])
+    # markerline, stemlines, baseline = ax.stem(freqs[pltrange], np.abs(yin[pltrange]), '-.')
+    # plt.setp(baseline, 'linewidth', 0)
+    # plt.setp(stemlines, 'color', 'g')
+    # plt.setp(markerline, 'markerfacecolor', 'g', 'markeredgecolor', 'g')
+    # ax.plot(freqs[pltrange], np.abs(yin[pltrange]), 'g', lw=2)
+    # ax.set_title('Input admittance (magnitude)')
+    # ax.set_xlabel('Frequency [Hz]')
+    # ax.set_ylabel('Admittance [Siemens]')
+    # ax.set_xlim([0.88e9, 1.02e9])
+    # ax.set_ylim([0, 0.035])
    # ax.grid()
-    #
+
    # Plot input admittance (phase)
-    #ax = plt.subplot(gs2[2, 1])
-    #markerline, stemlines, baseline = ax.stem(freqs[pltrange], np.angle(yin[pltrange], deg=True), '-.')
-    #plt.setp(baseline, 'linewidth', 0)
-    #plt.setp(stemlines, 'color', 'g')
-    #plt.setp(markerline, 'markerfacecolor', 'g', 'markeredgecolor', 'g')
-    #ax.plot(freqs[pltrange], np.angle(yin[pltrange], deg=True), 'g', lw=2)
-    #ax.set_title('Input admittance (phase)')
-    #ax.set_xlabel('Frequency [Hz]')
-    #ax.set_ylabel('Phase [degrees]')
-    ##ax.set_xlim([0.88e9, 1.02e9])
-    ##ax.set_ylim([-40, 100])
+    # ax = plt.subplot(gs2[2, 1])
+    # markerline, stemlines, baseline = ax.stem(freqs[pltrange], np.angle(yin[pltrange], deg=True), '-.')
+    # plt.setp(baseline, 'linewidth', 0)
+    # plt.setp(stemlines, 'color', 'g')
+    # plt.setp(markerline, 'markerfacecolor', 'g', 'markeredgecolor', 'g')
+    # ax.plot(freqs[pltrange], np.angle(yin[pltrange], deg=True), 'g', lw=2)
+    # ax.set_title('Input admittance (phase)')
+    # ax.set_xlabel('Frequency [Hz]')
+    # ax.set_ylabel('Phase [degrees]')
+    # ax.set_xlim([0.88e9, 1.02e9])
+    # ax.set_ylim([-40, 100])
    # ax.grid()

    # Save a PDF/PNG of the figure
-    #fig1.savefig(os.path.splitext(os.path.abspath(filename))[0] + '_tl_params.png', dpi=150, format='png', bbox_inches='tight', pad_inches=0.1)
-    #fig2.savefig(os.path.splitext(os.path.abspath(filename))[0] + '_ant_params.png', dpi=150, format='png', bbox_inches='tight', pad_inches=0.1)
-    #fig1.savefig(os.path.splitext(os.path.abspath(filename))[0] + '_tl_params.pdf', dpi=None, format='pdf', bbox_inches='tight', pad_inches=0.1)
-    #fig2.savefig(os.path.splitext(os.path.abspath(filename))[0] + '_ant_params.pdf', dpi=None, format='pdf', bbox_inches='tight', pad_inches=0.1)
+    # fig1.savefig(os.path.splitext(os.path.abspath(filename))[0] + '_tl_params.png', dpi=150, format='png', bbox_inches='tight', pad_inches=0.1)
+    # fig2.savefig(os.path.splitext(os.path.abspath(filename))[0] + '_ant_params.png', dpi=150, format='png', bbox_inches='tight', pad_inches=0.1)
+    # fig1.savefig(os.path.splitext(os.path.abspath(filename))[0] + '_tl_params.pdf', dpi=None, format='pdf', bbox_inches='tight', pad_inches=0.1)
+    # fig2.savefig(os.path.splitext(os.path.abspath(filename))[0] + '_ant_params.pdf', dpi=None, format='pdf', bbox_inches='tight', pad_inches=0.1)

    return plt

--- a/tools/plot_source_wave.py
+++ b/tools/plot_source_wave.py
@@ -156,8 +156,8 @@ def mpl_plot(w, timewindow, dt, iterations, fft=False):
    [ax.grid() for ax in fig.axes]  # Turn on grid

    # Save a PDF/PNG of the figure
-    #fig.savefig(os.path.dirname(os.path.abspath(__file__)) + os.sep + w.type + '.pdf', dpi=None, format='pdf', bbox_inches='tight', pad_inches=0.1)
-    #fig.savefig(os.path.dirname(os.path.abspath(__file__)) + os.sep + w.type + '.png', dpi=150, format='png', bbox_inches='tight', pad_inches=0.1)
+    # fig.savefig(os.path.dirname(os.path.abspath(__file__)) + os.sep + w.type + '.pdf', dpi=None, format='pdf', bbox_inches='tight', pad_inches=0.1)
+    # fig.savefig(os.path.dirname(os.path.abspath(__file__)) + os.sep + w.type + '.png', dpi=150, format='png', bbox_inches='tight', pad_inches=0.1)

    return plt

--- a/user_libs/antenna_patterns/initial_save.py
+++ b/user_libs/antenna_patterns/initial_save.py
@@ -25,7 +25,7 @@ outputfile = args.outputfile
 ########################################
 # User configurable parameters

-# Pattern type (E or H)
+# Pattern type (E or H)
 type = 'H'

 # Antenna (true if using full antenna model; false for a theoretical Hertzian dipole
@@ -116,21 +116,21 @@ for rx in range(0, nrx):
 f.close()

 # Plot traces for sanity checking
-#fig, ((ax1, ax2), (ax3, ax4), (ax5, ax6)) = plt.subplots(num=outputfile, nrows=3, ncols=2, sharex=False, sharey='col', subplot_kw=dict(xlabel='Time [ns]'), figsize=(20, 10), facecolor='w', edgecolor='w')
-#ax1.plot(time, Ex[:, traceno],'r', lw=2)
-#ax1.set_ylabel('$E_x$, field strength [V/m]')
-#ax3.plot(time, Ey[:, traceno],'r', lw=2)
-#ax3.set_ylabel('$E_y$, field strength [V/m]')
-#ax5.plot(time, Ez[:, traceno],'r', lw=2)
-#ax5.set_ylabel('$E_z$, field strength [V/m]')
-#ax2.plot(time, Hx[:, traceno],'b', lw=2)
-#ax2.set_ylabel('$H_x$, field strength [A/m]')
-#ax4.plot(time, Hy[:, traceno],'b', lw=2)
-#ax4.set_ylabel('$H_y$, field strength [A/m]')
-#ax6.plot(time, Hz[:, traceno],'b', lw=2)
-#ax6.set_ylabel('$H_z$, field strength [A/m]')
+# fig, ((ax1, ax2), (ax3, ax4), (ax5, ax6)) = plt.subplots(num=outputfile, nrows=3, ncols=2, sharex=False, sharey='col', subplot_kw=dict(xlabel='Time [ns]'), figsize=(20, 10), facecolor='w', edgecolor='w')
+# ax1.plot(time, Ex[:, traceno],'r', lw=2)
+# ax1.set_ylabel('$E_x$, field strength [V/m]')
+# ax3.plot(time, Ey[:, traceno],'r', lw=2)
+# ax3.set_ylabel('$E_y$, field strength [V/m]')
+# ax5.plot(time, Ez[:, traceno],'r', lw=2)
+# ax5.set_ylabel('$E_z$, field strength [V/m]')
+# ax2.plot(time, Hx[:, traceno],'b', lw=2)
+# ax2.set_ylabel('$H_x$, field strength [A/m]')
+# ax4.plot(time, Hy[:, traceno],'b', lw=2)
+# ax4.set_ylabel('$H_y$, field strength [A/m]')
+# ax6.plot(time, Hz[:, traceno],'b', lw=2)
+# ax6.set_ylabel('$H_z$, field strength [A/m]')
 # Turn on grid
-#[ax.grid() for ax in fig.axes]
+# [ax.grid() for ax in fig.axes]
 # plt.show()

 # Calculate fields for patterns
--- a/user_libs/antenna_patterns/plot_fields.py
+++ b/user_libs/antenna_patterns/plot_fields.py
@@ -18,15 +18,15 @@ from gprMax.constants import c, z0
 # Parse command line arguments
 parser = argparse.ArgumentParser(description='Plot field patterns from a simulation with receivers positioned in circles around an antenna. This module should be used after the field pattern data has been processed and stored using the initial_save.py module.', usage='cd gprMax; python -m user_libs.antenna_patterns.plot_fields numpyfile')
 parser.add_argument('numpyfile', help='name of numpy file including path')
-#parser.add_argument('hertzian', help='name of numpy file including path')
+# parser.add_argument('hertzian', help='name of numpy file including path')
 args = parser.parse_args()
 patterns = np.load(args.numpyfile)
-#hertzian = np.load(args.hertzian)
+# hertzian = np.load(args.hertzian)

 ########################################
 # User configurable parameters

-# Pattern type (E or H)
+# Pattern type (E or H)
 type = 'H'

 # Relative permittivity of half-space for homogeneous materials (set to None for inhomogeneous)
@@ -87,11 +87,11 @@ for patt in range(0, len(radii)):

 # Add Hertzian dipole plot
 # hertzplot1 = np.append(hertzian[0, :], hertzian[0, 0]) # Append start value to close circle
-#hertzplot1 = hertzplot1 / np.max(np.max(hertzian))
-#ax.plot(theta, 10 * np.log10(hertzplot1), label='Inf. dipole, 0.1m', color='black', ls='-.', lw=3)
+# hertzplot1 = hertzplot1 / np.max(np.max(hertzian))
+# ax.plot(theta, 10 * np.log10(hertzplot1), label='Inf. dipole, 0.1m', color='black', ls='-.', lw=3)
 # hertzplot2 = np.append(hertzian[-1, :], hertzian[-1, 0]) # Append start value to close circle
-#hertzplot2 = hertzplot2 / np.max(np.max(hertzian))
-#ax.plot(theta, 10 * np.log10(hertzplot2), label='Inf. dipole, 0.58m', color='black', ls='--', lw=3)
+# hertzplot2 = hertzplot2 / np.max(np.max(hertzian))
+# ax.plot(theta, 10 * np.log10(hertzplot2), label='Inf. dipole, 0.58m', color='black', ls='--', lw=3)

 # Theta axis options
 ax.set_theta_zero_location('N')
@@ -110,13 +110,13 @@ ax.set_yticklabels(yticks)
 ax.grid(True)
 handles, existlabels = ax.get_legend_handles_labels()
 leg = ax.legend([handles[0], handles[-1]], [existlabels[0], existlabels[-1]], ncol=2, loc=(0.27, -0.12), frameon=False)  # Plot just first and last legend entries
-#leg = ax.legend([handles[0], handles[-3], handles[-2], handles[-1]], [existlabels[0], existlabels[-3], existlabels[-2], existlabels[-1]], ncol=4, loc=(-0.13,-0.12), frameon=False)
+# leg = ax.legend([handles[0], handles[-3], handles[-2], handles[-1]], [existlabels[0], existlabels[-3], existlabels[-2], existlabels[-1]], ncol=4, loc=(-0.13,-0.12), frameon=False)
 [legobj.set_linewidth(2) for legobj in leg.legendHandles]

 # Save a pdf of the plot
 savename = os.path.splitext(args.numpyfile)[0] + '.pdf'
 fig.savefig(savename, dpi=None, format='pdf', bbox_inches='tight', pad_inches=0.1)
-#savename = os.path.splitext(args.numpyfile)[0] + '.png'
-#fig.savefig(savename, dpi=150, format='png', bbox_inches='tight', pad_inches=0.1)
+# savename = os.path.splitext(args.numpyfile)[0] + '.png'
+# fig.savefig(savename, dpi=150, format='png', bbox_inches='tight', pad_inches=0.1)

 plt.show()
--- a/user_libs/antennas.py
+++ b/user_libs/antennas.py
@@ -52,13 +52,13 @@ def antenna_like_GSSI_1500(x, y, z, resolution=0.001, rotate90=False, **kwargs):
    else:
        # excitationfreq = 1.5e9 # GHz
        # sourceresistance = 50 # Ohms
-        #absorberEr = 1.7
-        #absorbersig = 0.59
+        # absorberEr = 1.7
+        # absorbersig = 0.59

        # Values from http://hdl.handle.net/1842/4074
        excitationfreq = 1.71e9
-        #sourceresistance = 4
-        sourceresistance = 230  #  Correction for old (< 123) GprMax3D bug
+        # sourceresistance = 4
+        sourceresistance = 230  # Correction for old (< 123) GprMax3D bug
        absorberEr = 1.58
        absorbersig = 0.428
        rxres = 925  # Resistance at Rx bowtie
@@ -157,8 +157,8 @@ def antenna_like_GSSI_1500(x, y, z, resolution=0.001, rotate90=False, **kwargs):
    box(x, y, z, x + casesize[0], y + casesize[1], z + skidthickness, 'hdpe', rotate90origin=rotate90origin)

    # Geometry views
-    #geometry_view(x - dx, y - dy, z - dz, x + casesize[0] + dx, y + casesize[1] + dy, z + skidthickness + casesize[2] + dz, dx, dy, dz, 'antenna_like_GSSI_1500')
-    #geometry_view(x, y, z, x + casesize[0], y + casesize[1], z + 0.010, dx, dy, dz, 'antenna_like_GSSI_1500_pcb', type='f')
+    # geometry_view(x - dx, y - dy, z - dz, x + casesize[0] + dx, y + casesize[1] + dy, z + skidthickness + casesize[2] + dz, dx, dy, dz, 'antenna_like_GSSI_1500')
+    # geometry_view(x, y, z, x + casesize[0], y + casesize[1], z + 0.010, dx, dy, dz, 'antenna_like_GSSI_1500_pcb', type='f')

    # Excitation - custom pulse
    # print('#excitation_file: {}'.format(os.path.join(moduledirectory, 'GSSIgausspulse1.txt')))
@@ -395,8 +395,8 @@ def antenna_like_MALA_1200(x, y, z, resolution=0.001, rotate90=False, **kwargs):
    box(x, y, z + polypropylenethickness, x + casesize[0], y + casesize[1], z + polypropylenethickness + hdpethickness, 'hdpe', rotate90origin=rotate90origin)

    # Geometry views
-    #geometry_view(x - dx, y - dy, z - dz, x + casesize[0] + dx, y + casesize[1] + dy, z + casesize[2] + skidthickness + dz, dx, dy, dz, 'antenna_like_MALA_1200')
-    #geometry_view(x, y, z, x + casesize[0], y + casesize[1], z + 0.010, dx, dy, dz, 'antenna_like_MALA_1200_pcb', type='f')
+    # geometry_view(x - dx, y - dy, z - dz, x + casesize[0] + dx, y + casesize[1] + dy, z + casesize[2] + skidthickness + dz, dx, dy, dz, 'antenna_like_MALA_1200')
+    # geometry_view(x, y, z, x + casesize[0], y + casesize[1], z + 0.010, dx, dy, dz, 'antenna_like_MALA_1200_pcb', type='f')

    # Excitation
    print('#waveform: gaussian 1.0 {} myGaussian'.format(excitationfreq))
--- a/user_libs/optimisation_taguchi/fitness_functions.py
+++ b/user_libs/optimisation_taguchi/fitness_functions.py
@@ -107,31 +107,31 @@ def xcorr(filename, args):
        raise GeneralError('No outputs matching {} were found'.format(args['outputs']))

    # Normalise reference respose and response from output file
-#    refresp /= np.amax(np.abs(refresp))
-#    modelresp /= np.amax(np.abs(modelresp))
+    # refresp /= np.amax(np.abs(refresp))
+    # modelresp /= np.amax(np.abs(modelresp))

    # Make both responses the same length in time
-#    if reftime[-1] > modeltime[-1]:
-#        reftime = np.arange(0, f.attrs['dt'] * f.attrs['Iterations'], reftime[-1] / len(reftime))
-#        refresp = refresp[0:len(reftime)]
-#    elif modeltime[-1] > reftime[-1]:
-#        modeltime = np.arange(0, reftime[-1], f.attrs['dt'])
-#        modelresp = modelresp[0:len(modeltime)]
-#
-#    # Downsample the response with the higher sampling rate
-#    if len(modeltime) < len(reftime):
-#        refresp = signal.resample(refresp, len(modelresp))
-#    elif len(reftime) < len(modeltime):
-#        modelresp = signal.resample(modelresp, len(refresp))
+    # if reftime[-1] > modeltime[-1]:
+    #    reftime = np.arange(0, f.attrs['dt'] * f.attrs['Iterations'], reftime[-1] / len(reftime))
+    #    refresp = refresp[0:len(reftime)]
+    # elif modeltime[-1] > reftime[-1]:
+    #    modeltime = np.arange(0, reftime[-1], f.attrs['dt'])
+    #    modelresp = modelresp[0:len(modeltime)]
+
+    # Downsample the response with the higher sampling rate
+    # if len(modeltime) < len(reftime):
+    #    refresp = signal.resample(refresp, len(modelresp))
+    # elif len(reftime) < len(modeltime):
+    #    modelresp = signal.resample(modelresp, len(refresp))

    # Prepare data for normalized cross-correlation
    refresp = (refresp - np.mean(refresp)) / (np.std(refresp) * len(refresp))
    modelresp = (modelresp - np.mean(modelresp)) / np.std(modelresp)

    # Plots responses for checking
-    #fig, ax = plt.subplots(subplot_kw=dict(xlabel='Iterations', ylabel='Voltage [V]'), figsize=(20, 10), facecolor='w', edgecolor='w')
-    #ax.plot(refresp,'r', lw=2, label='refresp')
-    #ax.plot(modelresp,'b', lw=2, label='modelresp')
+    # fig, ax = plt.subplots(subplot_kw=dict(xlabel='Iterations', ylabel='Voltage [V]'), figsize=(20, 10), facecolor='w', edgecolor='w')
+    # ax.plot(refresp,'r', lw=2, label='refresp')
+    # ax.plot(modelresp,'b', lw=2, label='modelresp')
    # ax.grid()
    # plt.show()

@@ -142,10 +142,10 @@ def xcorr(filename, args):
    xcorr = np.nan_to_num(xcorr)

    # Plot cross-correlation for checking
-#    fig, ax = plt.subplots(subplot_kw=dict(xlabel='Iterations', ylabel='Voltage [V]'), figsize=(20, 10), facecolor='w', edgecolor='w')
-#    ax.plot(xcorr,'r', lw=2, label='xcorr')
-#    ax.grid()
-#    plt.show()
+    # fig, ax = plt.subplots(subplot_kw=dict(xlabel='Iterations', ylabel='Voltage [V]'), figsize=(20, 10), facecolor='w', edgecolor='w')
+    # ax.plot(xcorr,'r', lw=2, label='xcorr')
+    # ax.grid()
+    # plt.show()

    xcorrmax = np.amax(xcorr)

@@ -237,15 +237,15 @@ def compactness(filename, args):
            # Amplitude ratio of the 1st to 3rd peak - hopefully be a measure of a compact envelope
            compactness = np.abs(outputdata[peaks[0]]) / np.abs(outputdata[peaks[2]])

-#            # Percentage of maximum value to measure compactness of signal
-#            durationthreshold = 2
-#            # Check if there is a peak/trough smaller than threshold
-#            durationthresholdexist = np.where(np.abs(outputdata[peaks]) < (peak * (durationthreshold / 100)))[0]
-#            if durationthresholdexist.size == 0:
-#                compactness = time[peaks[-1]]
-#            else:
-#                time2threshold = time[peaks[durationthresholdexist[0]]]
-#                compactness = time2threshold - time[min(peaks)]
+            # Percentage of maximum value to measure compactness of signal
+            # durationthreshold = 2
+            # Check if there is a peak/trough smaller than threshold
+            # durationthresholdexist = np.where(np.abs(outputdata[peaks]) < (peak * (durationthreshold / 100)))[0]
+            # if durationthresholdexist.size == 0:
+            #    compactness = time[peaks[-1]]
+            # else:
+            #    time2threshold = time[peaks[durationthresholdexist[0]]]
+            #    compactness = time2threshold - time[min(peaks)]

    # Check in case no outputs where found
    if not outputsused: