LoopStructural 1.6.1__py3-none-any.whl

LoopStructural/datasets/data/refolded_bb.txt

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LoopStructural/datasets/data/refolded_fold.csv

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+88,2570.097656,4184.378418,3399.674316,-0.466875,-0.622452,-0.628157,s0,
+0,4823.496582,5576.529297,3652.300781,0.999869,0.008587,0.013755,s2,
+1,4509.626953,7308.625,3793.699219,0.999753,-0.022182,0.001305,s2,
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+3,8717.802734,5402.157227,4271.78125,0.998713,0.032723,-0.038755,s2,
+4,6485.54248,1681.78894,4266.632813,0.999788,0.019579,0.006339,s2,
+5,7817.476074,2067.795166,4299.859375,0.999597,-0.027851,0.005413,s2,
+6,2996.549805,3739.016357,3479.988281,0.999855,0.005633,0.016068,s2,
+7,2894.746094,3217.271973,3423.878906,0.999659,0.025509,0.005496,s2,
+8,2114.25,2670.076172,3580.832031,0.998758,0.045024,-0.021359,s2,
+0,5000.0,100.0,100.0,,,,s1,0.0
+0,4723.504395,4748.135254,3588.621094,,,,s2,0.0

LoopStructural/datasets/data/tabular_intrusion.csv

@@ -0,0 +1,23 @@
+feature_name,X,Y,Z,coord,val,gx,gy,gz,intrusion_contact_type,intrusion_anisotropy,intrusion_side
+stratigraphy,0.00,0.00,2.00,,0,,,,,,
+stratigraphy,0.00,5.00,2.00,,0,,,,,,
+stratigraphy,5.00,0.00,2.00,,0,,,,,,
+stratigraphy,5.00,5.00,2.00,,0,,,,,,
+stratigraphy,2.50,2.50,2.00,,,0,0,1,,,
+tabular_intrusion,3.04,2.12,2.18,,,,,,roof,stratigraphy,
+tabular_intrusion,4.02,3.85,2.14,,,,,,roof,stratigraphy,TRUE
+tabular_intrusion,2.02,3.16,2.02,,,,,,roof,stratigraphy,
+tabular_intrusion,2.12,2.16,2.02,,,,,,roof,stratigraphy,
+tabular_intrusion,1.14,3.50,2.04,,,,,,roof,,TRUE
+tabular_intrusion,4.08,3.02,1.18,,,,,,floor,,TRUE
+tabular_intrusion,1.14,1.06,1.16,,,,,,floor,,TRUE
+tabular_intrusion,4.20,2.18,1.12,,,,,,floor,,TRUE
+tabular_intrusion,1.02,3.02,1.12,,,,,,floor,,TRUE
+tabular_intrusion_frame,2.00,2.00,2.00,0,,0,0,-1,,,
+tabular_intrusion_frame,3.00,1.00,2.00,0,,0,0,-1,,,
+tabular_intrusion_frame,1.00,3.00,2.00,0,,0,0,-1,,,
+tabular_intrusion_frame,3.00,2.00,1.00,1,0,,,,,,
+tabular_intrusion_frame,3.00,2.00,1.00,1,,0,1,0,,,
+tabular_intrusion_frame,2.50,1.00,1.00,2,0,,,,,,
+tabular_intrusion_frame,2.50,2.00,1.00,2,0,,,,,,
+tabular_intrusion_frame,2.50,2.00,1.00,2,,1,0,0,,,

LoopStructural/datatypes/__init__.py

@@ -0,0 +1,4 @@
+from ._surface import Surface
+from ._bounding_box import BoundingBox
+from ._point import ValuePoints, VectorPoints
+from ._structured_grid import StructuredGrid

LoopStructural/datatypes/_bounding_box.py

@@ -0,0 +1,422 @@
+from __future__ import annotations
+from typing import Optional, Union, Dict
+from LoopStructural.utils.exceptions import LoopValueError
+from LoopStructural.utils import rng
+from LoopStructural.datatypes._structured_grid import StructuredGrid
+import numpy as np
+
+from LoopStructural.utils.logging import getLogger
+
+logger = getLogger(__name__)
+
+
+class BoundingBox:
+    def __init__(
+        self,
+        origin: Optional[np.ndarray] = None,
+        maximum: Optional[np.ndarray] = None,
+        global_origin: Optional[np.ndarray] = None,
+        nsteps: Optional[np.ndarray] = None,
+        step_vector: Optional[np.ndarray] = None,
+        dimensions: Optional[int] = 3,
+    ):
+        """A bounding box for a model, defined by the
+        origin, maximum and number of steps in each direction
+
+        Parameters
+        ----------
+        dimensions : int, optional
+            _description_, by default 3
+        origin : Optional[np.ndarray], optional
+            _description_, by default None
+        maximum : Optional[np.ndarray], optional
+            _description_, by default None
+        nsteps : Optional[np.ndarray], optional
+            _description_, by default None
+        """
+        # reproject relative to the global origin, if origin is not provided.
+        # we want the local coordinates to start at 0
+        # otherwise uses provided origin. This is useful for having multiple bounding boxes rela
+        if global_origin is not None and origin is None:
+            origin = np.zeros(global_origin.shape)
+        if maximum is None and nsteps is not None and step_vector is not None:
+            maximum = origin + nsteps * step_vector
+        if origin is not None and global_origin is None:
+            global_origin = origin
+        self._origin = np.array(origin)
+        self._maximum = np.array(maximum)
+        self.dimensions = dimensions
+        if self.origin.shape:
+            if self.origin.shape[0] != self.dimensions:
+                logger.warning(
+                    f"Origin has {self.origin.shape[0]} dimensions but bounding box has {self.dimensions}"
+                )
+
+        else:
+            self.dimensions = dimensions
+        self._global_origin = global_origin
+        self.nsteps = np.array([50, 50, 25])
+        if nsteps is not None:
+            self.nsteps = np.array(nsteps)
+        self.name_map = {
+            "xmin": (0, 0),
+            "ymin": (0, 1),
+            "zmin": (0, 2),
+            "xmax": (1, 0),
+            "ymax": (1, 1),
+            "zmax": (1, 2),
+            "lower": (0, 2),
+            "upper": (1, 2),
+            "minx": (0, 0),
+            "miny": (0, 1),
+            "minz": (0, 2),
+            "maxx": (1, 0),
+            "maxy": (1, 1),
+            "maxz": (1, 2),
+        }
+
+    @property
+    def global_origin(self):
+        return self._global_origin
+
+    @global_origin.setter
+    def global_origin(self, global_origin):
+        if self.dimensions != len(global_origin):
+            logger.warning(
+                f"Global origin has {len(global_origin)} dimensions but bounding box has {self.dimensions}"
+            )
+        self._global_origin = global_origin
+
+    @property
+    def global_maximum(self):
+        return self.maximum - self.origin + self._global_origin
+
+    @property
+    def valid(self):
+        return self._origin is not None and self._maximum is not None
+
+    @property
+    def origin(self) -> np.ndarray:
+        if self._origin is None:
+            raise LoopValueError("Origin is not set")
+        return self._origin
+
+    @origin.setter
+    def origin(self, origin: np.ndarray):
+        if self.dimensions != len(origin):
+            logger.warning(
+                f"Origin has {len(origin)} dimensions but bounding box has {self.dimensions}"
+            )
+        self._origin = origin
+
+    @property
+    def maximum(self) -> np.ndarray:
+        if self._maximum is None:
+            raise LoopValueError("Maximum is not set")
+        return self._maximum
+
+    @maximum.setter
+    def maximum(self, maximum: np.ndarray):
+        self._maximum = maximum
+
+    @property
+    def nelements(self):
+        return self.nsteps.prod()
+
+    @property
+    def volume(self):
+        return np.prod(self.maximum - self.origin)
+
+    @property
+    def bb(self):
+        return np.array([self.origin, self.maximum])
+
+    @nelements.setter
+    def nelements(self, nelements: Union[int, float]):
+        """Update the number of elements in the associated grid
+        This is for visualisation, not for the interpolation
+        When set it will update the nsteps/step vector for cubic
+        elements
+
+        Parameters
+        ----------
+        nelements : int,float
+            The new number of elements
+        """
+        box_vol = self.volume
+        ele_vol = box_vol / nelements
+        # calculate the step vector of a regular cube
+        step_vector = np.zeros(self.dimensions)
+        step_vector[:] = ele_vol ** (1.0 / 3.0)
+        # number of steps is the length of the box / step vector
+        nsteps = np.ceil((self.maximum - self.origin) / step_vector).astype(int)
+        self.nsteps = nsteps
+
+    @property
+    def corners(self) -> np.ndarray:
+        """Returns the corners of the bounding box in local coordinates
+
+
+
+        Returns
+        -------
+        np.ndarray
+            array of corners in clockwise order
+        """
+
+        return np.array(
+            [
+                self.origin.tolist(),
+                [self.maximum[0], self.origin[1], self.origin[2]],
+                [self.maximum[0], self.maximum[1], self.origin[2]],
+                [self.origin[0], self.maximum[1], self.origin[2]],
+                [self.origin[0], self.origin[1], self.maximum[2]],
+                [self.maximum[0], self.origin[1], self.maximum[2]],
+                self.maximum.tolist(),
+                [self.origin[0], self.maximum[1], self.maximum[2]],
+            ]
+        )
+
+    @property
+    def corners_global(self) -> np.ndarray:
+        """Returns the corners of the bounding box
+        in the original space
+
+        Returns
+        -------
+        np.ndarray
+            corners of the bounding box
+        """
+        return np.array(
+            [
+                self.global_origin.tolist(),
+                [self.global_maximum[0], self.global_origin[1], self.global_origin[2]],
+                [self.global_maximum[0], self.global_maximum[1], self.global_origin[2]],
+                [self.global_origin[0], self.global_maximum[1], self.global_origin[2]],
+                [self.global_origin[0], self.global_origin[1], self.global_maximum[2]],
+                [self.global_maximum[0], self.global_origin[1], self.global_maximum[2]],
+                self.global_maximum.tolist(),
+                [self.global_origin[0], self.global_maximum[1], self.global_maximum[2]],
+            ]
+        )
+
+    @property
+    def step_vector(self):
+        return (self.maximum - self.origin) / self.nsteps
+
+    @property
+    def length(self):
+        return self.maximum - self.origin
+
+    def fit(self, locations: np.ndarray, local_coordinate: bool = False) -> BoundingBox:
+        """Initialise the bounding box from a set of points.
+
+        Parameters
+        ----------
+        locations : np.ndarray
+            xyz locations of the points to fit the bbox
+        local_coordinate : bool, optional
+            whether to set the origin to [0,0,0], by default False
+
+        Returns
+        -------
+        BoundingBox
+            A reference to the bounding box object, note this is not a new bounding box
+            it updates the current one in place.
+
+        Raises
+        ------
+        LoopValueError
+            _description_
+        """
+        if locations.shape[1] != self.dimensions:
+            raise LoopValueError(
+                f"locations array is {locations.shape[1]}D but bounding box is {self.dimensions}"
+            )
+        origin = locations.min(axis=0)
+        maximum = locations.max(axis=0)
+        if local_coordinate:
+            self.global_origin = origin
+            self.origin = np.zeros(3)
+            self.maximum = maximum - origin
+        else:
+            self.origin = origin
+            self.maximum = maximum
+            self.global_origin = np.zeros(3)
+        return self
+
+    def with_buffer(self, buffer: float = 0.2) -> BoundingBox:
+        """Create a new bounding box with a buffer around the existing bounding box
+
+        Parameters
+        ----------
+        buffer : float, optional
+            percentage to expand the dimensions by, by default 0.2
+
+        Returns
+        -------
+        BoundingBox
+            The new bounding box object.
+
+        Raises
+        ------
+        LoopValueError
+            if the current bounding box is invalid
+        """
+        if self.origin is None or self.maximum is None:
+            raise LoopValueError("Cannot create bounding box with buffer, no origin or maximum")
+        # local coordinates, rescale into the original bounding boxes global coordinates
+        origin = self.origin - buffer * (self.maximum - self.origin)
+        maximum = self.maximum + buffer * (self.maximum - self.origin)
+        return BoundingBox(
+            origin=origin, maximum=maximum, global_origin=self.global_origin + origin
+        )
+
+    def get_value(self, name):
+        ix, iy = self.name_map.get(name, (-1, -1))
+        if ix == -1 and iy == -1:
+            raise LoopValueError(f"{name} is not a valid bounding box name")
+        if iy == -1:
+            return self.origin[ix]
+
+        return self.bb[ix,]
+
+    def __getitem__(self, name):
+        if isinstance(name, str):
+            return self.get_value(name)
+        elif isinstance(name, tuple):
+            return self.origin
+        return self.get_value(name)
+
+    def is_inside(self, xyz):
+        xyz = np.array(xyz)
+        if len(xyz.shape) == 1:
+            xyz = xyz.reshape((1, -1))
+        if xyz.shape[1] != 3:
+            raise LoopValueError(
+                f"locations array is {xyz.shape[1]}D but bounding box is {self.dimensions}"
+            )
+        inside = np.ones(xyz.shape[0], dtype=bool)
+        inside = np.logical_and(inside, xyz[:, 0] > self.origin[0])
+        inside = np.logical_and(inside, xyz[:, 0] < self.maximum[0])
+        inside = np.logical_and(inside, xyz[:, 1] > self.origin[1])
+        inside = np.logical_and(inside, xyz[:, 1] < self.maximum[1])
+        inside = np.logical_and(inside, xyz[:, 2] > self.origin[2])
+        inside = np.logical_and(inside, xyz[:, 2] < self.maximum[2])
+        return inside
+
+    def regular_grid(
+        self,
+        nsteps: Optional[Union[list, np.ndarray]] = None,
+        shuffle: bool = False,
+        order: str = "C",
+        local: bool = True,
+    ) -> np.ndarray:
+        """Get the grid of points from the bounding box
+
+        Parameters
+        ----------
+        nsteps : Optional[Union[list, np.ndarray]], optional
+            number of steps, by default None uses self.nsteps
+        shuffle : bool, optional
+            Whether to return points in order or random, by default False
+        order : str, optional
+            when flattening using numpy "C" or "F", by default "C"
+        local : bool, optional
+            Whether to return the points in the local coordinate system of global
+            , by default True
+
+        Returns
+        -------
+        np.ndarray
+            numpy array N,3 of the points
+        """
+
+        if nsteps is None:
+            nsteps = self.nsteps
+        coordinates = [
+            np.linspace(self.origin[i], self.maximum[i], nsteps[i]) for i in range(self.dimensions)
+        ]
+
+        if not local:
+            coordinates = [
+                np.linspace(self.global_origin[i], self.global_maximum[i], nsteps[i])
+                for i in range(self.dimensions)
+            ]
+        coordinate_grid = np.meshgrid(*coordinates, indexing="ij")
+        locs = np.array([coord.flatten(order=order) for coord in coordinate_grid]).T
+
+        if shuffle:
+            # logger.info("Shuffling points")
+            rng.shuffle(locs)
+        return locs
+
+    def cell_centers(self, order: str = "F") -> np.ndarray:
+        """Get the cell centers of a regular grid
+
+        Parameters
+        ----------
+        order : str, optional
+            order of the grid, by default "C"
+
+        Returns
+        -------
+        np.ndarray
+            array of cell centers
+        """
+        locs = self.regular_grid(order=order, nsteps=self.nsteps - 1)
+
+        return locs + 0.5 * self.step_vector
+
+    def to_dict(self) -> dict:
+        """Export the defining characteristics of the bounding
+        box to a dictionary for json serialisation
+
+        Returns
+        -------
+        dict
+            dictionary with origin, maximum and nsteps
+        """
+        return {
+            "origin": self.origin.tolist(),
+            "maximum": self.maximum.tolist(),
+            "nsteps": self.nsteps.tolist(),
+        }
+
+    def vtk(self):
+        """Export the model as a pyvista RectilinearGrid
+
+        Returns
+        -------
+        pv.RectilinearGrid
+            a pyvista grid object
+
+        Raises
+        ------
+        ImportError
+            If pyvista is not installed raise import error
+        """
+        try:
+            import pyvista as pv
+        except ImportError:
+            raise ImportError("pyvista is required for vtk support")
+        x = np.linspace(self.global_origin[0], self.global_maximum[0], self.nsteps[0])
+        y = np.linspace(self.global_origin[1], self.global_maximum[1], self.nsteps[1])
+        z = np.linspace(self.global_origin[2], self.global_maximum[2], self.nsteps[2])
+        return pv.RectilinearGrid(
+            x,
+            y,
+            z,
+        )
+
+    def structured_grid(
+        self, cell_data: Dict[str, np.ndarray] = {}, vertex_data={}, name: str = "bounding_box"
+    ):
+        return StructuredGrid(
+            origin=self.global_origin,
+            step_vector=self.step_vector,
+            nsteps=self.nsteps,
+            cell_properties=cell_data,
+            properties=vertex_data,
+            name=name,
+        )