docs: updating examples and deps

Author: lachlangrose

docs/requirements.txt

@@ -1,5 +1,6 @@
-sphinx==3.5.4
+sphinx
 sphinx_gallery
 sphinxcontrib-bibtex
 pydata_sphinx_theme
-myst-parser
+myst-parser
+sphinx-design

docs/source/index.rst

@@ -90,29 +90,24 @@ constraints.
     # load in a dataframe with x,y,z,val,nx,ny,nz to constrain the value and
     # gradient normal of the interpolator
     data, bb = load_claudius()
-    # create a transformer to move the data to the centre of mass of the dataset
-    # this avoid any numerical issues caused by large coordinates. This dataset
-    # is already axis aligned so we don't need to rotate the data but we can rotate it
-    # so that the main anisotropy of the dataset is aligned with the x axis.
-    transformer = EuclideanTransformation(dimensions=3, fit_rotation=False).fit(
-        data[["X", "Y", "Z"]]
-    )
-    data[["X", "Y", "Z"]] = transformer.transform(data[["X", "Y", "Z"]])
+
     # Find the bounding box of the data by finding the extent
     bounding_box = BoundingBox().fit(data[["X", "Y", "Z"]])
     # assemble an interpolator using the bounding box and the data
     interpolator = (
-        InterpolatorBuilder(interpolatortype="FDI", bounding_box=bounding_box)
+        InterpolatorBuilder(
+            interpolatortype="FDI", bounding_box=bounding_box.with_buffer(0.1)
+        )
         .add_value_constraints(data.loc[data["val"].notna(), ["X", "Y", "Z", "val"]].values)
         .add_normal_constraints(
             data.loc[data["nx"].notna(), ["X", "Y", "Z", "nx", "ny", "nz"]].values
-        ).build()
+        )
+        .build()
     )
     # Set the number of elements in the bounding box to 10000 and create a structured grid
     bounding_box.nelements = 10000
     mesh = bounding_box.structured_grid()
     # add the interpolated values to the mesh at the nodes
-    # mesh.properties["v"] = interpolator.evaluate_value(bounding_box.regular_grid(order='F'))
     mesh.properties["v"] = interpolator.evaluate_value(mesh.nodes)
 
     # or the cell centres

examples/1_basic/plot_2_surface_modelling.py

@@ -123,7 +123,7 @@
 # Visualize Model Surfaces
 # ~~~~~~~~~~~~~~~~~~~~~~~~
 # Plot the surfaces of the geological model using a 3D viewer.
-
+print(model.stratigraphic_column.to_dict())
 viewer = Loop3DView(model)
 viewer.plot_model_surfaces(cmap="tab20")
 viewer.display()

examples/1_basic/plot_3_model_visualisation.py

@@ -121,8 +121,8 @@
 
 
 viewer.plot_scalar_field(strati, cmap="prism")
-print(viewer._build_stratigraphic_cmap(model))
-viewer.plot_block_model()
+# print(viewer._build_stratigraphic_cmap(model))
+viewer.plot_block_model(cmap='tab20')
 # Add the data addgrad/addvalue arguments are optional
 viewer.plot_data(strati, vector=True, value=True)
 viewer.display()  # to add an interactive display

examples/2_fold/plot_1_adding_folds_to_surfaces.py

@@ -147,7 +147,7 @@
 #                       'box',
 #                      paint_with=stratigraphy,
 #                      cmap='prism')
-viewer.plot_data(stratigraphy, scale=200)
+viewer.plot_data(stratigraphy)
 viewer.plot_surface(stratigraphy, value=10)
 viewer.show()
 
@@ -190,6 +190,8 @@
 # fold limb rotation angle is found by finding the the angle to rotate the
 # folded foliation to be parallel to the plane of the axial foliation
 # shown in B and C.
+# The wavelength can be specified by the user or in some cases estimated
+# from the s-variogram of the fold frame coordinate system.
 #
 mdata = pd.concat([data[:npoints], data[data["feature_name"] == "s1"]])
 model = GeologicalModel(boundary_points[0, :], boundary_points[1, :])
@@ -202,10 +204,10 @@
 )
 stratigraphy = model.create_and_add_folded_foliation(
     "s0",
-    fold_frame,
+    fold_frame=fold_frame,
     nelements=10000,
     fold_axis=[-6.51626577e-06, -5.00013645e-01, -8.66017526e-01],
-    #                                                    limb_wl=1
+    limb_wl=12000,
     buffer=0.5,
 )
 viewer = Loop3DView(model, background="white")
@@ -220,7 +222,7 @@
     #                       isovalue=0.4,
     opacity=0.5,
 )
-viewer.plot_data(stratigraphy, scale=200)
+viewer.plot_data(stratigraphy)
 # viewer.add_isosurface(fold_frame[1],colour='green',alpha=0.5)
 # viewer.add_vector_field(fold_frame[0],locations=fold_frame[0].get_interpolator().support.barycentre)
 # viewer.add_data(fold_frame[1])
@@ -234,6 +236,7 @@
 # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 rotation_plots = RotationAnglePlotter(stratigraphy)
 rotation_plots.add_fold_limb_data()
+rotation_plots.add_limb_svariogram()
 # plt.plot(stratigraphy.builder.fold.fold_limb_rotation.fold_frame_coordinate,stratigraphy['limb_rotation'],'bo')
 # x = np.linspace(fold_frame[0].min(),fold_frame[0].max(),100)
 # plt.plot(x,stratigraphy['fold'].fold_limb_rotation(x),'r--')

examples/2_fold/_refolded_folds.py examples/2_fold/plot_2__refolded_folds.pyexamples/2_fold/_refolded_folds.py renamed to examples/2_fold/plot_2__refolded_folds.py

@@ -6,6 +6,7 @@
 """
 
 from LoopStructural import GeologicalModel
+from LoopStructural.modelling.features import fold
 from LoopStructural.visualisation import Loop3DView, RotationAnglePlotter
 from LoopStructural.datasets import load_laurent2016
 import pandas as pd
@@ -36,10 +37,9 @@
 model.set_model_data(data)
 s2 = model.create_and_add_fold_frame("s2", nelements=10000, buffer=0.5, solver="lu", damp=True)
 viewer = Loop3DView(model)
-viewer.add_scalar_field(s2[0], cmap="prism")
-viewer.add_isosurface(s2[0], slices=[0, 1])
-viewer.add_data(s2[0])
-viewer.rotate(rotation)
+viewer.plot_scalar_field(s2[0], cmap="prism")
+viewer.plot_surface(s2[0], [0, 1])
+viewer.plot_data(s2[0])
 viewer.display()
 
 
@@ -48,12 +48,13 @@
 # ~~~~~~~~~~~~
 #
 
-s1 = model.create_and_add_folded_fold_frame("s1", av_fold_axis=True, nelements=50000, buffer=0.3)
+s1 = model.create_and_add_folded_fold_frame(
+    "s1", fold_frame=s2, av_fold_axis=True, nelements=50000, buffer=0.3, limb_wl=4
+)
 
 
 viewer = Loop3DView(model)
-viewer.add_scalar_field(s1[0], cmap="prism")
-viewer.rotate([-69.11979675292969, 15.704944610595703, 6.00014591217041])
+viewer.plot_scalar_field(s1[0], cmap="prism")
 viewer.display()
 
 ######################################################################
@@ -77,14 +78,14 @@
 
 s0 = model.create_and_add_folded_foliation(
     "s0",
+    fold_frame=s1,
     av_fold_axis=True,
     nelements=50000,
     buffer=0.2,
 )
 
 viewer = Loop3DView(model)
-viewer.add_scalar_field(s0, cmap="tab20")
-viewer.rotate([-69.11979675292969, 15.704944610595703, 6.00014591217041])
+viewer.plot_scalar_field(s0, cmap="tab20")
 viewer.display()
 
 ######################################################################
@@ -102,8 +103,7 @@
 # ax[1].plot(s0['limb_svariogram'].lags,s1['limb_svariogram'].variogram,'bo')
 
 viewer = Loop3DView(model)
-viewer.add_isosurface(s0, nslices=10, paint_with=s0, cmap="tab20")
+viewer.plot_surface(s0, 10, paint_with=s0, cmap="tab20")
 # viewer.add_data(s0)
 # viewer.add_fold(s0['fold'],locations=s0['support'].barycentre[::80])
-viewer.rotate([-69.11979675292969, 15.704944610595703, 6.00014591217041])
 viewer.display()