Dev gemgis2

docs/conf.py

@@ -25,6 +25,7 @@
 
 # The full version, including alpha/beta/rc tags
 release = '1.0.3'
+version = release
 
 # -- GemGIS configuration ---------------------------------------------------
 sys.path.append('../../gemgis')
@@ -37,7 +38,7 @@
 # ones.
 extensions = [
     'nbsphinx',
-    'sphinx_rtd_theme',
+    "sphinx_book_theme",
     #'sphinx.ext.autodoc',
     'sphinx.ext.napoleon',
     'sphinx.ext.doctest',
@@ -63,13 +64,24 @@
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
-html_theme = 'sphinx_rtd_theme'
+html_theme = "sphinx_book_theme"
 
 # 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 = []
 
+html_title = "GemGIS - Spatial data processing for geomodeling"
+html_logo = "https://raw.githubusercontent.com/cgre-aachen/gemgis/main/docs/getting_started/images/Modern1.png"
+html_favicon = "https://raw.githubusercontent.com/cgre-aachen/gemgis/main/docs/getting_started/images/facvon.ico"
+
+#html_theme_options = {
+#    "repository_url": "https://github.com/cgre-aachen/gemgis",
+#    "use_repository_button": True,
+#    "use_issues_button": True,
+#    "use_edit_page_button": True,
+#}
+
 nbsphinx_execute = 'never'
 
 nbsphinx_execute_arguments = [
@@ -79,3 +91,9 @@
 
 copybutton_prompt_text = ">>> "
 
+
+
+# General information about the project.
+project = "GemGIS"
+copyright = "2020–2023, GemGIS Developers"
+

docs/getting_started/about.rst

@@ -1,4 +1,5 @@
-.. gemgis documentation master file, created by
+.. _about_ref:
+gemgis documentation master file, created by
    sphinx-quickstart on Mon Nov  2 22:04:17 2020.
    You can adapt this file completely to your liking, but it should at least
    contain the root `toctree` directive.

docs/getting_started/example/example30.ipynb

@@ -1678,7 +1678,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# Adding additional orientations"
+    "## Adding additional orientations"
    ]
   },
   {
@@ -2257,7 +2257,7 @@
  "metadata": {
   "hide_input": false,
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -2271,7 +2271,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.5"
+   "version": "3.10.8"
   },
   "latex_envs": {
    "LaTeX_envs_menu_present": true,

docs/getting_started/example/index.rst

@@ -6,7 +6,7 @@ Example Models
 There is a series of examples available for GemGIS. In order to keep the size of the main GemGIS package as small as possible, the data is provided through a separated repository `gemgis-data <https://github.com/cgre-aachen/gemgis_data/tree/main>`_. You can also download the data directly following `this link <https://github.com/cgre-aachen/gemgis_data/archive/main.zip>`_.
 
 .. toctree::
-    :maxdepth: 2
+    :maxdepth: 1
     :caption: Examples
 
     example01

docs/getting_started/installation.rst

@@ -107,16 +107,6 @@ In order to visualize and work with meshes, the `PyVista <https://docs.pyvista.o
     conda install -c conda-forge pyvista">=0.37.0"
 
 
-Installing GemPy (Optional)
-~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-The current modeling package that is supported by GemGIS is `GemPy <https://docs.gempy.org/>`_. GemPy can easily be installed with ``pip``/PyPi::
-
-   pip install gempy
-
-.. image:: images/cmd7.png
-
-
 Installing GemGIS via PyPi
 ~~~~~~~~~~~~~~~~~~~~~~~~~~
 
@@ -148,7 +138,7 @@ Use the following command to go up one level in your folder structure::
 
    cd ..
 
-Now, a new git repository needs to be initiated within the gemgis folder:
+Now, a new git repository needs to be initiated within the gemgis folder::
 
    git init
 
@@ -164,6 +154,15 @@ You should now have the latest GemGIS files in your gemgis folder.
 
 .. image:: images/cmd10.png
 
+Installing GemPy (Optional)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+The current modeling package that is supported by GemGIS is `GemPy <https://docs.gempy.org/>`_. GemPy can easily be installed with ``pip``/PyPi::
+
+   pip install gempy
+
+.. image:: images/cmd7.png
+
 Checking the Installation
 ~~~~~~~~~~~~~~~~~~~~~~~~~
 

docs/getting_started/tutorial/index.rst

@@ -33,7 +33,7 @@ Each set of functions of GemGIS is collected in a different module. The function
 
 
 .. toctree::
-    :maxdepth: 2
+    :maxdepth: 1
     :caption: Tutorials
 
     00_generating_data_qgis
@@ -74,7 +74,7 @@ Each set of functions of GemGIS is collected in a different module. The function
     35_plotting_borehole_data_with_pyvista
     36_creating_proj_crs_objects_for_gemgis
     37_delaunay_triangulation_for_isoline_maps
-    38_interactive_plotting_with_bokeh_ingemgis
+    38_interactive_plotting_with_bokeh_in_gemgis
     39_shapely_base_geometries_with_z_component
     40_working_with_gpx_data_in_gemgis
     41_working_with_kml_data
@@ -93,4 +93,5 @@ Each set of functions of GemGIS is collected in a different module. The function
     54_converting_pyvista_mesh_to_zmap_grid
     55_extracting_well_tops_from_pyvista_meshes
     56_Displaying_Seismic_Data_in_Pyvista
-    57_creating_spaghetti_plots_in_gempy
+    57_creating_spaghetti_plots_in_gempy
+    58_creating_hexagonal_grid

docs/index.rst

@@ -3,11 +3,23 @@
    You can adapt this file completely to your liking, but it should at least
    contain the root `toctree` directive.
 
-Welcome to documentation page of GemGIS - GemPy Geographic!
+Welcome to the documentation page of GemGIS |version|!
 ===========================================================
 
+
+GemGIS is a Python-based, open-source geographic information processing library. It is capable of preprocessing spatial data such as vector data (shape files, geojson files, geopackages,...), raster data (tif, png,...), data obtained from online services (WCS, WMS, WFS) or XML/KML files (soon). Preprocessed data can be stored in a dedicated Data Class to be passed to the geomodeling package `GemPy <https://github.com/cgre-aachen/gempy>`_ in order to accelerate the model building process. Postprocessing of model results will allow export from GemPy to geoinformation systems such as QGIS and ArcGIS or to Google Earth for further use.
+
+GemGIS uses and combines the full functionality of `GeoPandas <https://geopandas.org/>`_, `rasterio <https://rasterio.readthedocs.io/en/latest/>`_, `OWSLib <https://geopython.github.io/OWSLib/>`_, `Pandas <https://pandas.pydata.org/docs/>`_, `Shapely <https://shapely.readthedocs.io/en/latest/manual.html>`_,  `PyVista <https://docs.pyvista.org/>`_ and `NumPy <https://numpy.org/>`_ to simplify, accelerate and automate the workflows used to preprocess spatial data for geomodeling.
+
+
+.. container:: button
+
+    :doc:`About GemGIS <getting_started/about>` | :doc:`Installation <getting_started/installation>` |
+    :doc:`Tutorials <getting_started/tutorial/index>` | :doc:`Examples <getting_started/example/index>`
+
 .. toctree::
-   :maxdepth: 3
+   :hidden:
+   :maxdepth: 2
    :caption: Getting Started
    :glob:
 
@@ -21,16 +33,6 @@ Welcome to documentation page of GemGIS - GemPy Geographic!
    getting_started/tutorial/index
    getting_started/example/index
 
-
-
-
-
-
-
-
-
-
-
 Indices and tables
 ==================
 

environment_dev.yml

@@ -19,6 +19,7 @@ dependencies:
     - sphinx_markdown_tables
     - sphinx_gallery
     - sphinx_rtd_theme
+    - sphinx_book_theme
     - sphinx_copybutton
     - sphinx_automodapi
     - sphinx_numfig

gemgis/utils.py

@@ -553,7 +553,7 @@ def show_number_of_data_points(geo_model):  # gp.core.model.Project):
     # Add columns to geo_model surface table
     gdf['No. of Interfaces'] = no_int
     gdf['No. of Orientations'] = no_ori
-    
+
     return gdf
 
 
@@ -1811,7 +1811,7 @@ def convert_to_petrel_points_with_attributes(mesh: pv.core.pointset.PolyData,
     print('CSV-File successfully saved')
 
 
-def ray_trace_one_surface(surface: pv.core.pointset.PolyData,
+def ray_trace_one_surface(surface: Union[pv.core.pointset.PolyData, pv.core.pointset.UnstructuredGrid],
                           origin: Union[np.ndarray, list],
                           end_point: Union[np.ndarray, list],
                           first_point: bool = False) -> tuple:
@@ -1820,8 +1820,8 @@ def ray_trace_one_surface(surface: pv.core.pointset.PolyData,
     Parameters:
     ___________
 
-        surface: pv.core.pointset.PolyData
-            Calculated GemPy surface
+        surface: Union[pv.core.pointset.PolyData, pv.core.pointset.UnstructuredGrid]
+            Calculated or clipped GemPy surface
 
         origin:
             Coordinates of the top of the well
@@ -1834,6 +1834,14 @@ def ray_trace_one_surface(surface: pv.core.pointset.PolyData,
 
     """
 
+    # Checking that the provided surface is of type PoyData or UnstructuredGrid
+    if not isinstance(surface, (pv.core.pointset.PolyData, pv.core.pointset.UnstructuredGrid)):
+        raise TypeError('Surface must be provided as PolyData or UnstructuredGrid')
+
+    # Converting UnstructuredGrid to PolyData
+    if isinstance(surface, pv.core.pointset.UnstructuredGrid):
+        surface = surface.extract_surface()
+
     # Extracting the intersection between a PolyData set and a mesh
     intersection_points, intersection_cells = surface.ray_trace(origin=origin,
                                                                 end_point=end_point,