LoopStructural 1.6.8__tar.gz → 1.6.10__tar.gz

{loopstructural-1.6.8 → loopstructural-1.6.10}/LoopStructural/datatypes/_bounding_box.py

@@ -326,7 +326,9 @@ class BoundingBox:
         if iy == -1:
             return self.origin[ix]
 
-        return self.bb[ix,]
+        return self.bb[
+            ix,
+        ]
 
     def __getitem__(self, name):
         if isinstance(name, str):
@@ -430,6 +432,26 @@ class BoundingBox:
             "nsteps": self.nsteps.tolist(),
         }
 
+    @classmethod
+    def from_dict(cls, data: dict) -> 'BoundingBox':
+        """Create a bounding box from a dictionary
+
+        Parameters
+        ----------
+        data : dict
+            dictionary with origin, maximum and nsteps
+
+        Returns
+        -------
+        BoundingBox
+            bounding box object
+        """
+        return cls(
+            origin=np.array(data["origin"]),
+            maximum=np.array(data["maximum"]),
+            nsteps=np.array(data["nsteps"]),
+        )
+
     def vtk(self):
         """Export the model as a pyvista RectilinearGrid
 

{loopstructural-1.6.8 → loopstructural-1.6.10}/LoopStructural/datatypes/_surface.py

@@ -1,5 +1,5 @@
 from dataclasses import dataclass, field
-from typing import Optional
+from typing import Optional, Union
 import numpy as np
 import io
 from LoopStructural.utils import getLogger
@@ -11,6 +11,8 @@ logger = getLogger(__name__)
 class Surface:
     vertices: np.ndarray = field(default_factory=lambda: np.array([[0, 0, 0]]))
     triangles: np.ndarray = field(default_factory=lambda: np.array([[0, 0, 0]]))
+    colour: Optional[Union[str, np.ndarray]] = field(default_factory=lambda: None)
+
     normals: Optional[np.ndarray] = None
     name: str = 'surface'
     values: Optional[np.ndarray] = None

{loopstructural-1.6.8 → loopstructural-1.6.10}/LoopStructural/interpolators/_finite_difference_interpolator.py

@@ -272,12 +272,7 @@ class FiniteDifferenceInterpolator(DiscreteInterpolator):
             idc[inside, :] = gi[node_idx[inside, :]]
             inside = np.logical_and(~np.any(idc == -1, axis=1), inside)
 
-            (
-                vertices,
-                T,
-                elements,
-                inside_,
-            ) = self.support.get_element_gradient_for_location(
+            (vertices, T, elements, inside_,) = self.support.get_element_gradient_for_location(
                 points[inside, : self.support.dimension]
             )
             # normalise constraint vector and scale element matrix by this
@@ -340,12 +335,7 @@ class FiniteDifferenceInterpolator(DiscreteInterpolator):
             # calculate unit vector for node gradients
             # this means we are only constraining direction of grad not the
             # magnitude
-            (
-                vertices,
-                T,
-                elements,
-                inside_,
-            ) = self.support.get_element_gradient_for_location(
+            (vertices, T, elements, inside_,) = self.support.get_element_gradient_for_location(
                 points[inside, : self.support.dimension]
             )
             # T*=np.product(self.support.step_vector)
@@ -432,12 +422,7 @@ class FiniteDifferenceInterpolator(DiscreteInterpolator):
             vectors[norm > 0, :] /= norm[norm > 0, None]
 
             # normalise element vector to unit vector for dot product
-            (
-                vertices,
-                T,
-                elements,
-                inside_,
-            ) = self.support.get_element_gradient_for_location(
+            (vertices, T, elements, inside_,) = self.support.get_element_gradient_for_location(
                 points[inside, : self.support.dimension]
             )
             T[norm > 0, :, :] /= norm[norm > 0, None, None]

{loopstructural-1.6.8 → loopstructural-1.6.10}/LoopStructural/interpolators/supports/_3d_base_structured.py

@@ -162,9 +162,9 @@ class BaseStructuredSupport(BaseSupport):
         length = self.maximum - origin
         length /= self.step_vector
         self._nsteps = np.ceil(length).astype(np.int64)
-        self._nsteps[self._nsteps == 0] = (
-            3  # need to have a minimum of 3 elements to apply the finite difference mask
-        )
+        self._nsteps[
+            self._nsteps == 0
+        ] = 3  # need to have a minimum of 3 elements to apply the finite difference mask
         if np.any(~(self._nsteps > 0)):
             logger.error(
                 f"Cannot resize the interpolation support. The proposed number of steps is {self._nsteps}, these must be all > 0"

{loopstructural-1.6.8 → loopstructural-1.6.10}/LoopStructural/interpolators/supports/_3d_structured_tetra.py

@@ -166,9 +166,9 @@ class TetMesh(BaseStructuredSupport):
         shared_face_index[:] = -1
         shared_face_index[row.reshape(-1, 3)[:, 0], :] = col.reshape(-1, 3)
 
-        self.shared_elements[np.arange(self.shared_element_relationships.shape[0]), :] = (
-            shared_face_index
-        )
+        self.shared_elements[
+            np.arange(self.shared_element_relationships.shape[0]), :
+        ] = shared_face_index
         # resize
         self.shared_elements = self.shared_elements[: len(self.shared_element_relationships), :]
 

{loopstructural-1.6.8 → loopstructural-1.6.10}/LoopStructural/interpolators/supports/_3d_unstructured_tetra.py

@@ -173,9 +173,9 @@ class UnStructuredTetMesh(BaseSupport):
         shared_face_index[:] = -1
         shared_face_index[row.reshape(-1, 3)[:, 0], :] = col.reshape(-1, 3)
 
-        self.shared_elements[np.arange(self.shared_element_relationships.shape[0]), :] = (
-            shared_face_index
-        )
+        self.shared_elements[
+            np.arange(self.shared_element_relationships.shape[0]), :
+        ] = shared_face_index
         # resize
         self.shared_elements = self.shared_elements[: len(self.shared_element_relationships), :]
         # flag = np.zeros(self.elements.shape[0])

{loopstructural-1.6.8 → loopstructural-1.6.10}/LoopStructural/interpolators/supports/_face_table.py

@@ -63,8 +63,8 @@ def _init_face_table(grid):
     shared_face_index = np.zeros((shared_faces.shape[0], grid.dimension), dtype=int)
     shared_face_index[:] = -1
     shared_face_index[row.reshape(-1, grid.dimension)[:, 0], :] = col.reshape(-1, grid.dimension)
-    grid._shared_elements[np.arange(grid.shared_element_relationships.shape[0]), :] = (
-        shared_face_index
-    )
+    grid._shared_elements[
+        np.arange(grid.shared_element_relationships.shape[0]), :
+    ] = shared_face_index
     # resize
     grid._shared_elements = grid.shared_elements[: len(grid.shared_element_relationships), :]

{loopstructural-1.6.8 → loopstructural-1.6.10}/LoopStructural/modelling/core/geological_model.py

@@ -598,10 +598,12 @@ class GeologicalModel:
                 * self._data.loc[mask, "polarity"].to_numpy()[:, None]
             )
             self._data.drop(["strike", "dip"], axis=1, inplace=True)
-        self._data[['X', 'Y', 'Z', 'val', 'nx', 'ny', 'nz', 'gx', 'gy', 'gz', 'tx', 'ty', 'tz']] = (
-            self._data[
-                ['X', 'Y', 'Z', 'val', 'nx', 'ny', 'nz', 'gx', 'gy', 'gz', 'tx', 'ty', 'tz']
-            ].astype(float)
+        self._data[
+            ['X', 'Y', 'Z', 'val', 'nx', 'ny', 'nz', 'gx', 'gy', 'gz', 'tx', 'ty', 'tz']
+        ] = self._data[
+            ['X', 'Y', 'Z', 'val', 'nx', 'ny', 'nz', 'gx', 'gy', 'gz', 'tx', 'ty', 'tz']
+        ].astype(
+            float
         )
 
     def set_model_data(self, data):
@@ -1293,6 +1295,7 @@ class GeologicalModel:
         fault_trace_anisotropy=0.0,
         fault_dip=90,
         fault_dip_anisotropy=0.0,
+        fault_pitch=None,
         **kwargs,
     ):
         """
@@ -1379,6 +1382,7 @@ class GeologicalModel:
             major_axis = major_axis / self.scale_factor
         if intermediate_axis:
             intermediate_axis = intermediate_axis / self.scale_factor
+        print(fault_dip, fault_normal_vector)
         fault_frame_builder.create_data_from_geometry(
             fault_frame_data=fault_frame_data,
             fault_center=fault_center,
@@ -1393,6 +1397,7 @@ class GeologicalModel:
             fault_trace_anisotropy=fault_trace_anisotropy,
             fault_dip=fault_dip,
             fault_dip_anisotropy=fault_dip_anisotropy,
+            fault_pitch=fault_pitch,
         )
         if "force_mesh_geometry" not in kwargs:
             fault_frame_builder.set_mesh_geometry(kwargs.get("fault_buffer", 0.2), 0)
@@ -1798,7 +1803,10 @@ class GeologicalModel:
             values = values.loc[~np.logical_or(values == np.inf, values == -np.inf)]
             surfaces.extend(
                 self.get_feature_by_name(u).surfaces(
-                    values.to_list(), self.bounding_box, name=names.loc[values.index].to_list()
+                    values.to_list(),
+                    self.bounding_box,
+                    name=names.loc[values.index].to_list(),
+                    colours=unit_table.loc[unit_table['feature_name'] == u, 'colour'].tolist(),
                 )
             )
 

{loopstructural-1.6.8 → loopstructural-1.6.10}/LoopStructural/modelling/features/_base_geological_feature.py

@@ -274,6 +274,7 @@ class BaseFeature(metaclass=ABCMeta):
         value: Union[float, int, List[Union[float, int]]],
         bounding_box=None,
         name: Optional[Union[List[str], str]] = None,
+        colours: Optional[Union[str, np.ndarray]] = None,
     ) -> surface_list:
         """Find the surfaces of the geological feature at a given value
 
@@ -305,7 +306,7 @@ class BaseFeature(metaclass=ABCMeta):
             isosurfacer = LoopIsosurfacer(bounding_box, callable=callable)
             if name is None and self.name is not None:
                 name = self.name
-            surfaces = isosurfacer.fit(value, name)
+            surfaces = isosurfacer.fit(value, name, colours=colours)
         except Exception as e:
             logger.error(f"Failed to create surface for {self.name} at value {value}")
             logger.error(e)
@@ -333,9 +334,13 @@ class BaseFeature(metaclass=ABCMeta):
                 raise ValueError("Must specify bounding box")
             bounding_box = self.model.bounding_box
         grid = bounding_box.structured_grid(name=self.name)
-        value = self.evaluate_value(
-            self.model.scale(bounding_box.regular_grid(local=False, order='F'))
-        )
+        value = self.evaluate_value(bounding_box.regular_grid(local=False, order='F'))
+        if self.model is not None:
+
+            value = self.evaluate_value(
+                self.model.scale(bounding_box.regular_grid(local=False, order='F'))
+            )
+
         grid.properties[self.name] = value
 
         value = self.evaluate_value(bounding_box.cell_centres(order='F'))

{loopstructural-1.6.8 → loopstructural-1.6.10}/LoopStructural/modelling/features/_geological_feature.py

@@ -42,6 +42,7 @@ class GeologicalFeature(BaseFeature):
         builder,
         regions: list = [],
         faults: list = [],
+        interpolator=None,
         model=None,
     ):
         """Default constructor for geological feature
@@ -60,7 +61,7 @@ class GeologicalFeature(BaseFeature):
         BaseFeature.__init__(self, name, model, faults, regions, builder)
         self.name = name
         self.builder = builder
-        self.interpolator = self.builder.interpolator if self.builder is not None else None
+        self.interpolator = self.builder.interpolator if self.builder is not None else interpolator
         self.type = FeatureType.INTERPOLATED
 
     def to_json(self):

{loopstructural-1.6.8 → loopstructural-1.6.10}/LoopStructural/modelling/features/_lambda_geological_feature.py

@@ -90,3 +90,14 @@ class LambdaGeologicalFeature(BaseFeature):
 
     def get_data(self, value_map: Optional[dict] = None):
         return
+
+    def copy(self, name: Optional[str] = None):
+        return LambdaGeologicalFeature(
+            self.function,
+            name if name is not None else f'{self.name}_copy',
+            self.gradient_function,
+            self.model,
+            self.regions,
+            self.faults,
+            self.builder,
+        )

{loopstructural-1.6.8 → loopstructural-1.6.10}/LoopStructural/modelling/features/builders/_fault_builder.py

@@ -91,6 +91,7 @@ class FaultBuilder(StructuralFrameBuilder):
         fault_trace_anisotropy=1.0,
         fault_dip=90,
         fault_dip_anisotropy=1.0,
+        fault_pitch=None,
     ):
         """Generate the required data for building a fault frame for a fault with the
         specified parameters
@@ -204,6 +205,7 @@ class FaultBuilder(StructuralFrameBuilder):
                 fault_frame_data["coord"] == 1, ~np.isnan(fault_frame_data["gz"])
             )
             fault_slip_data = fault_frame_data.loc[slip_mask, ["gx", "gy", "gz"]]
+
             if len(fault_slip_data) == 0:
                 logger.warning(
                     "There is no slip vector data for the fault, using vertical slip vector\n\
@@ -211,6 +213,11 @@ class FaultBuilder(StructuralFrameBuilder):
                 )
                 strike_vector, dip_vector = get_vectors(fault_normal_vector[None, :])
                 fault_slip_vector = dip_vector[:, 0]
+                if fault_pitch is not None:
+                    print('using pitch')
+                    rotm = rotation(fault_normal_vector[None,:],[fault_pitch])
+                    print(rotm.shape,fault_slip_vector.shape)
+                    fault_slip_vector = np.einsum("ijk,k->ij", rotm, fault_slip_vector)[0,:]
                 logger.info(f"Estimated fault slip vector: {fault_slip_vector}")
             else:
                 fault_slip_vector = fault_slip_data.mean(axis=0).to_numpy()

{loopstructural-1.6.8 → loopstructural-1.6.10}/LoopStructural/modelling/input/process_data.py

@@ -299,9 +299,9 @@ class ProcessInputData:
             pts = self.fault_locations.loc[
                 self.fault_locations["feature_name"] == fname, ["X", "Y", "Z"]
             ]
-            fault_properties.loc[fname, ["centreEasting", "centreNorthing", "centreAltitude"]] = (
-                np.nanmean(pts, axis=0)
-            )
+            fault_properties.loc[
+                fname, ["centreEasting", "centreNorthing", "centreAltitude"]
+            ] = np.nanmean(pts, axis=0)
         if (
             "avgNormalEasting" not in fault_properties.columns
             or "avgNormalNorthing" not in fault_properties.columns
@@ -449,9 +449,9 @@ class ProcessInputData:
         for _name, sg in self.stratigraphic_order:
             value = 0.0  # reset for each supergroup
             if sg[0] not in self.thicknesses or self.thicknesses[sg[0]] <= 0:
-                self.thicknesses[sg[0]] = (
-                    np.inf
-                )  # make the top unit infinite as it should extend to the top of the model
+                self.thicknesses[
+                    sg[0]
+                ] = np.inf  # make the top unit infinite as it should extend to the top of the model
             for g in reversed(
                 sg[:-1]
             ):  # don't add the last unit as we never see the base of this unit.

{loopstructural-1.6.8 → loopstructural-1.6.10}/LoopStructural/utils/_surface.py

@@ -64,6 +64,7 @@ class LoopIsosurfacer:
         values: Optional[Union[list, int, float]],
         name: Optional[Union[List[str], str]] = None,
         local=False,
+        colours: Optional[List] = None,
     ) -> surface_list:
         """Extract isosurfaces from the interpolator
 
@@ -120,7 +121,9 @@ class LoopIsosurfacer:
             names = [name] * len(isovalues)
         if isinstance(name, list):
             names = name
-        for name, isovalue in zip(names, isovalues):
+        if colours is None:
+            colours = [None] * len(isovalues)
+        for name, isovalue, colour in zip(names, isovalues, colours):
             try:
                 step_vector = (self.bounding_box.maximum - self.bounding_box.origin) / (
                     np.array(self.bounding_box.nsteps) - 1
@@ -150,6 +153,7 @@ class LoopIsosurfacer:
                     normals=normals,
                     name=f"{name}_{isovalue}",
                     values=values,
+                    colour=colour,
                 )
             )
         return surfaces

loopstructural-1.6.10/LoopStructural/version.py

@@ -0,0 +1 @@
+__version__ = "1.6.10"

{loopstructural-1.6.8 → loopstructural-1.6.10}/LoopStructural.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.2
+Metadata-Version: 2.4
 Name: LoopStructural
-Version: 1.6.8
+Version: 1.6.10
 Summary: 3D geological modelling
 Author-email: Lachlan Grose <lachlan.grose@monash.edu>
 License: MIT
@@ -29,12 +29,12 @@ Requires-Dist: scipy
 Requires-Dist: scikit-image
 Requires-Dist: scikit-learn
 Provides-Extra: all
-Requires-Dist: loopstructural[export,inequalities,visualisation]; extra == "all"
+Requires-Dist: loopstructural[export,inequalities,jupyter,visualisation]; extra == "all"
 Requires-Dist: tqdm; extra == "all"
 Provides-Extra: visualisation
 Requires-Dist: matplotlib; extra == "visualisation"
 Requires-Dist: pyvista; extra == "visualisation"
-Requires-Dist: loopstructuralviusualisation>0.1.4; extra == "visualisation"
+Requires-Dist: loopstructuralviusualisation>=0.1.14; extra == "visualisation"
 Provides-Extra: export
 Requires-Dist: geoh5py; extra == "export"
 Requires-Dist: pyevtk; extra == "export"
@@ -58,6 +58,7 @@ Requires-Dist: geopandas; extra == "docs"
 Requires-Dist: sphinxcontrib-bibtex; extra == "docs"
 Requires-Dist: myst-parser; extra == "docs"
 Requires-Dist: sphinx-design; extra == "docs"
+Dynamic: license-file
 
 # LoopStructural: Loop3D Implicit Geological Modelling
 

{loopstructural-1.6.8 → loopstructural-1.6.10}/LoopStructural.egg-info/requires.txt

@@ -5,7 +5,7 @@ scikit-image
 scikit-learn
 
 [all]
-loopstructural[export,inequalities,visualisation]
+loopstructural[export,inequalities,jupyter,visualisation]
 tqdm
 
 [docs]
@@ -38,4 +38,4 @@ pyvista[all]
 [visualisation]
 matplotlib
 pyvista
-loopstructuralviusualisation>0.1.4
+loopstructuralviusualisation>=0.1.14

{loopstructural-1.6.8 → loopstructural-1.6.10}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.2
+Metadata-Version: 2.4
 Name: LoopStructural
-Version: 1.6.8
+Version: 1.6.10
 Summary: 3D geological modelling
 Author-email: Lachlan Grose <lachlan.grose@monash.edu>
 License: MIT
@@ -29,12 +29,12 @@ Requires-Dist: scipy
 Requires-Dist: scikit-image
 Requires-Dist: scikit-learn
 Provides-Extra: all
-Requires-Dist: loopstructural[export,inequalities,visualisation]; extra == "all"
+Requires-Dist: loopstructural[export,inequalities,jupyter,visualisation]; extra == "all"
 Requires-Dist: tqdm; extra == "all"
 Provides-Extra: visualisation
 Requires-Dist: matplotlib; extra == "visualisation"
 Requires-Dist: pyvista; extra == "visualisation"
-Requires-Dist: loopstructuralviusualisation>0.1.4; extra == "visualisation"
+Requires-Dist: loopstructuralviusualisation>=0.1.14; extra == "visualisation"
 Provides-Extra: export
 Requires-Dist: geoh5py; extra == "export"
 Requires-Dist: pyevtk; extra == "export"
@@ -58,6 +58,7 @@ Requires-Dist: geopandas; extra == "docs"
 Requires-Dist: sphinxcontrib-bibtex; extra == "docs"
 Requires-Dist: myst-parser; extra == "docs"
 Requires-Dist: sphinx-design; extra == "docs"
+Dynamic: license-file
 
 # LoopStructural: Loop3D Implicit Geological Modelling
 

{loopstructural-1.6.8 → loopstructural-1.6.10}/pyproject.toml

@@ -41,8 +41,8 @@ dependencies = [
 dynamic = ['version']
 
 [project.optional-dependencies]
-all = ['loopstructural[visualisation,inequalities,export]', 'tqdm']
-visualisation = ["matplotlib", "pyvista", "loopstructuralviusualisation>0.1.4"]
+all = ['loopstructural[visualisation,inequalities,export,jupyter]', 'tqdm']
+visualisation = ["matplotlib", "pyvista", "loopstructuralviusualisation>=0.1.14"]
 export = ["geoh5py", "pyevtk", "dill"]
 jupyter = ["pyvista[all]"]
 inequalities = ["loopsolver"]

loopstructural-1.6.8/LoopStructural/version.py

@@ -1 +0,0 @@
-__version__ = "1.6.8"