Modem updates

docs/source/conf.py

@@ -14,23 +14,24 @@
 #
 import os
 import sys
-sys.path.insert(0, os.path.abspath('.'))
-sys.path.insert(0, os.path.abspath('..'))
-sys.path.insert(0, os.path.abspath('../..'))
+
+sys.path.insert(0, os.path.abspath("."))
+sys.path.insert(0, os.path.abspath(".."))
+sys.path.insert(0, os.path.abspath("../.."))
 print(sys.path)
 
-os.environ['GDAL_DATA'] ='/tmp'
+os.environ["GDAL_DATA"] = "/tmp"
 
 # -- Project information -----------------------------------------------------
 
-project = u'mtpy'
-copyright = u'2018, Geoscience Australia'
-author = u'Alison Kirkby, Fei Zhang, Jared Peacock, Rakib Hassan, Jingming Duan'
+project = u"mtpy"
+copyright = u"2018, Geoscience Australia"
+author = u"Alison Kirkby, Fei Zhang, Jared Peacock, Rakib Hassan, Jingming Duan"
 
 # The short X.Y version
-version = u'1.01'
+version = u"1.01"
 # The full version, including alpha/beta/rc tags
-release = u'1.01.01'
+release = u"1.01.01"
 
 
 # -- General configuration ---------------------------------------------------
@@ -43,36 +44,36 @@
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = [
- 'sphinx.ext.autodoc',
- 'sphinx.ext.doctest',
- 'sphinx.ext.coverage',
- 'sphinx.ext.imgmath',
- 'sphinx.ext.viewcode',
- 'numpydoc',
- 'sphinx.ext.autosummary',
- 'sphinx.ext.githubpages',
+ "sphinx.ext.autodoc",
+ "sphinx.ext.doctest",
+ "sphinx.ext.coverage",
+ "sphinx.ext.imgmath",
+ "sphinx.ext.viewcode",
+ "numpydoc",
+ "sphinx.ext.autosummary",
+ "sphinx.ext.githubpages",
 ]
 
 extensions += [
  #'matplotlib.sphinxext.only_directives',
  #'matplotlib.sphinxext.plot_directive',
  # 'matplotlib.sphinxext.ipython_directive',
  # 'matplotlib.sphinxext.ipython_console_highlighting'
- ]
+]
 
 
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['templates']
+templates_path = ["templates"]
 
 # The suffix(es) of source filenames.
 # You can specify multiple suffix as a list of string:
 #
 # source_suffix = ['.rst', '.md']
-source_suffix = '.rst'
+source_suffix = ".rst"
 
 # The master toctree document.
-master_doc = 'index'
-#master_doc = 'master_doc'
+master_doc = "index"
+# master_doc = 'master_doc'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
@@ -87,7 +88,7 @@
 exclude_patterns = []
 
 # The name of the Pygments (syntax highlighting) style to use.
-pygments_style = 'sphinx'
+pygments_style = "sphinx"
 
 
 # -- Options for HTML output -------------------------------------------------
@@ -96,7 +97,7 @@
 # a list of builtin themes.
 #
 # html_theme = 'alabaster'
-html_theme = 'classic'
+html_theme = "classic"
 
 
 # Theme options are theme-specific and customize the look and feel of a theme
@@ -108,7 +109,7 @@
 # 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,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['static']
+html_static_path = ["static"]
 
 # Custom sidebar templates, must be a dictionary that maps document names
 # to template names.
@@ -124,7 +125,7 @@
 # -- Options for HTMLHelp output ---------------------------------------------
 
 # Output file base name for HTML help builder.
-htmlhelp_basename = 'mtpydoc'
+htmlhelp_basename = "mtpydoc"
 
 
 # -- Options for LaTeX output ------------------------------------------------
@@ -133,15 +134,12 @@
  # The paper size ('letterpaper' or 'a4paper').
  #
  # 'papersize': 'letterpaper',
-
  # The font size ('10pt', '11pt' or '12pt').
  #
  # 'pointsize': '10pt',
-
  # Additional stuff for the LaTeX preamble.
  #
  # 'preamble': '',
-
  # Latex figure (float) alignment
  #
  # 'figure_align': 'htbp',
@@ -151,19 +149,15 @@
 # (source start file, target name, title,
 # author, documentclass [howto, manual, or own class]).
 latex_documents = [
- (master_doc, 'mtpy.tex', u'MTPy Documentation',
- author, 'manual'),
+ (master_doc, "mtpy.tex", u"MTPy Documentation", author, "manual"),
 ]
 
 
 # -- Options for manual page output ------------------------------------------
 
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
-man_pages = [
- (master_doc, 'mtpy', u'mtpy Documentation',
- [author], 1)
-]
+man_pages = [(master_doc, "mtpy", u"mtpy Documentation", [author], 1)]
 
 
 # -- Options for Texinfo output ----------------------------------------------
@@ -172,9 +166,15 @@
 # (source start file, target name, title, author,
 # dir menu entry, description, category)
 texinfo_documents = [
- (master_doc, 'mtpy', u'mtpy Documentation',
- author, 'mtpy', 'One line description of project.',
- 'Miscellaneous'),
+ (
+ master_doc,
+ "mtpy",
+ u"mtpy Documentation",
+ author,
+ "mtpy",
+ "One line description of project.",
+ "Miscellaneous",
+ ),
 ]
 
 
@@ -196,7 +196,7 @@
 # epub_uid = ''
 
 # A list of files that should not be packed into the epub file.
-epub_exclude_files = ['search.html']
+epub_exclude_files = ["search.html"]
 
 
 # -- Extension configuration -------------------------------------------------
@@ -207,12 +207,12 @@
 # mod = __import__(extname, None, None, ['setup'])
 # RuntimeError: sys.path must be a list of directory names
 # See: http://read-the-docs.readthedocs.org/en/latest/faq.html#i-get-import-errors-on-libraries-that-depend-on-c-modules
-#NATIVE_MODULES = [
+# NATIVE_MODULES = [
 MOCK_MODULES = [
- 'osgeo',
- 'osgeo.ogr',
- 'osgeo.gdal',
- 'osgeo.osr',
+ "osgeo",
+ "osgeo.ogr",
+ "osgeo.gdal",
+ "osgeo.osr",
 ]
 
 import mock
@@ -221,7 +221,7 @@
  sys.modules[mod_name] = mock.Mock()
 
 
-#sys.modules.update([(mod_name, Mock()) for mod_name in NATIVE_MODULES])
+# sys.modules.update([(mod_name, Mock()) for mod_name in NATIVE_MODULES])
 # sys.modules['rasterio.coords'].BoundingBox = Mock
 # sphinx\registry.py", line 315, in load_extension
 # mod = __import__(extname, None, None, ['setup'])

examples/cmdline/build_ModEM_inputfiles.py

@@ -50,8 +50,9 @@ def build_modem_inputfiles(edi_path, output_path):
  start_period = 0.002
  stop_period = 2000
  periods_per_decade = 4
- period_list = get_period_list(start_period, stop_period, periods_per_decade,
- include_outside_range=True)
+ period_list = get_period_list(
+ start_period, stop_period, periods_per_decade, include_outside_range=True
+ )
 
  ## an example to use the periods from a particular edi file
  # edifile_periods = op.join(edipath,'Synth00.edi')
@@ -62,56 +63,65 @@ def build_modem_inputfiles(edi_path, output_path):
  workdir = output_path
  edipath = edi_path
  # list of edi files, search for all files ending with '.edi'
- edi_list = [op.join(edipath, ff) for ff in os.listdir(edipath) if (ff.endswith('.edi'))]
+ edi_list = [
+ op.join(edipath, ff) for ff in os.listdir(edipath) if (ff.endswith(".edi"))
+ ]
 
  # make the save path if it doesn't exist
  if not op.exists(workdir):
  os.mkdir(workdir)
 
- do = Data(edi_list=edi_list,
- inv_mode='1',
- save_path=workdir,
- period_list=period_list,
- period_buffer=2, # factor to stretch interpolation by. For example: if period_buffer=2
- # then interpolated data points will only be included if they are
- # within a factor of 2 of a true data point
- error_type_z=np.array([['floor_percent', 'floor_egbert'],
- # error type, options are 'egbert', 'percent', 'mean_od', 'eigen', 'median', 'off_diagonals'
- ['floor_egbert', 'percent']]), # add floor to apply it as an error floor
- # can supply a 2 x 2 array for each component or a single value
- error_value_z=np.array([[20., 5.], # error floor value in percent
- [5., 20.]]), # can supply a 2 x 2 array for each component or a single value
- error_type_tipper='floor_abs', # type of error to set in tipper,
- # floor_abs is an absolute value set as a floor
- error_value_tipper=.03,
- model_epsg=28354 # model epsg, currently set to utm zone 54.
- # See http://spatialreference.org/ to find the epsg code for your projection
- )
+ do = Data(
+ edi_list=edi_list,
+ inv_mode="1",
+ save_path=workdir,
+ period_list=period_list,
+ period_buffer=2, # factor to stretch interpolation by. For example: if period_buffer=2
+ # then interpolated data points will only be included if they are
+ # within a factor of 2 of a true data point
+ error_type_z=np.array(
+ [
+ ["floor_percent", "floor_egbert"],
+ # error type, options are 'egbert', 'percent', 'mean_od', 'eigen', 'median', 'off_diagonals'
+ ["floor_egbert", "percent"],
+ ]
+ ), # add floor to apply it as an error floor
+ # can supply a 2 x 2 array for each component or a single value
+ error_value_z=np.array(
+ [[20.0, 5.0], [5.0, 20.0]] # error floor value in percent
+ ), # can supply a 2 x 2 array for each component or a single value
+ error_type_tipper="floor_abs", # type of error to set in tipper,
+ # floor_abs is an absolute value set as a floor
+ error_value_tipper=0.03,
+ model_epsg=28354 # model epsg, currently set to utm zone 54.
+ # See http://spatialreference.org/ to find the epsg code for your projection
+ )
  do.write_data_file()
 
  # set elevations to zero as we need to ensure the stations are on the topography
- do.data_array['elev'] = 0.
+ do.data_array["elev"] = 0.0
  do.write_data_file(fill=False)
 
  # create model file
- mo = Model(station_locations=do.station_locations,
- cell_size_east=8000,
- cell_size_north=8000,
- pad_north=7, # number of padding cells in each of the north and south directions
- pad_east=7, # number of east and west padding cells
- pad_z=6, # number of vertical padding cells
- pad_stretch_v=1.6, # factor to increase by in padding cells (vertical)
- pad_stretch_h=1.4, # factor to increase by in padding cells (horizontal)
- pad_num=3, # number of constant-width cells to add to outside of model before padding cells start
- # this number is currently multiplied by 1.5 internally
- n_air_layers=10, # number of air layers, set to 0 to incorporate bathymetry only
- res_model=100, # halfspace resistivity value for reference model
- n_layers=100, # total number of z layers, including air
- z1_layer=10, # first layer thickness
- pad_method='stretch', # method for calculating padding
- z_mesh_method='new',
- z_target_depth=120000 # depth to bottom of core model (padding after this depth)
- )
+ mo = Model(
+ station_locations=do.station_locations,
+ cell_size_east=8000,
+ cell_size_north=8000,
+ pad_north=7, # number of padding cells in each of the north and south directions
+ pad_east=7, # number of east and west padding cells
+ pad_z=6, # number of vertical padding cells
+ pad_stretch_v=1.6, # factor to increase by in padding cells (vertical)
+ pad_stretch_h=1.4, # factor to increase by in padding cells (horizontal)
+ pad_num=3, # number of constant-width cells to add to outside of model before padding cells start
+ # this number is currently multiplied by 1.5 internally
+ n_air_layers=10, # number of air layers, set to 0 to incorporate bathymetry only
+ res_model=100, # halfspace resistivity value for reference model
+ n_layers=100, # total number of z layers, including air
+ z1_layer=10, # first layer thickness
+ pad_method="stretch", # method for calculating padding
+ z_mesh_method="new",
+ z_target_depth=120000, # depth to bottom of core model (padding after this depth)
+ )
 
  mo.make_mesh()
  mo.write_model_file(save_path=workdir)
@@ -120,7 +130,9 @@ def build_modem_inputfiles(edi_path, output_path):
  # if the number of air layers is zero - bathymetry only will be added.
  # if the number of air layers is nonzero - topography will be added, discretised into that number of cells
  # mo.add_topography_to_model2(r'C:\mtpywin\mtpy\examples\data\AussieContinent_etopo1.asc')
- mo.add_topography_to_model2(r'C:\Githubz\mtpy\examples\data\AussieContinent_etopo1.asc')
+ mo.add_topography_to_model2(
+ r"C:\Githubz\mtpy\examples\data\AussieContinent_etopo1.asc"
+ )
  mo.write_model_file(save_path=workdir)
 
  # update data elevations
@@ -143,9 +155,11 @@ def build_modem_inputfiles(edi_path, output_path):
 # ====================================================================================================
 if __name__ == "__main__":
 
- USAGE = "\n********************************************\n " \
- "Usage: python %s edi_dir_path output_dir_path " \
- "\n********************************************\n " % sys.argv[0]
+ USAGE = (
+ "\n********************************************\n "
+ "Usage: python %s edi_dir_path output_dir_path "
+ "\n********************************************\n " % sys.argv[0]
+ )
 
  if len(sys.argv) < 3:
  print(USAGE)