resfo-utilities 0.0.1__py3-none-any.whl → 0.0.3__py3-none-any.whl

resfo_utilities/_cornerpoint_grid.py

@@ -1,11 +1,11 @@
 from __future__ import annotations
 import os
-from typing import Self, Any, IO, TypeVar
+from typing import Self, Any, IO, TypeVar, Callable
 from dataclasses import dataclass
 from numpy import typing as npt
 import numpy as np
 import resfo
-import trimesh
+import scipy.optimize
 import warnings
 from matplotlib.path import Path
 import heapq
@@ -72,7 +72,7 @@ class MapAxes:
 @dataclass
 class CornerpointGrid:
     """
-    A :term:`corner-point grid` is a tessellation of a 3D volumne where
+    A :term:`corner-point grid` is a tessellation of a 3D volume where
     each cell is a hexahedron.
 
     Each cell is identified by a integer coordinate (i,j,k).
@@ -92,14 +92,15 @@ class CornerpointGrid:
             of the i,j pillar and coord[i,j,1] is the corresponding bottom end point.
         zcorn:
             A (ni, nj, nk, 8) array where zcorn[i,j,k] is the z value of
-            the 8 corners of the cell at i,j,k.
+            the 8 corners of the cell at i,j,k. The order of the corner z values
+            are as follows:
+            [TSW, TSE, TNW, TNE, BSW, BSE, BNW, BNE] where N(orth) means higher y,
+            E(east) means higher x, T(op) means lower z (when z is interpreted as depth).
 
         map_axes:
             Optionally each point is interpreted to be relative to some map
             coordinate system. Defaults to the unit coordinate system with
-            origo at (0,0). The order of the corner z valus are as follows:
-            [TSW, TSE, TNW, TNE, BSW, BSE, BNW, BNE] where N(orth) means higher y,
-            E(east) means higer x, T(op) means lower z (when z is interpreted as depth).
+            origin at (0,0).
 
     """
 
@@ -117,7 +118,7 @@ class CornerpointGrid:
 
         Args:
             file_like:
-                The EGRID file, could either be a filename, patlike or an opened
+                The EGRID file, could either be a filename, pathlike or an opened
                 EGRID file. The function also handles formatted egrid files (.FEGRID).
                 Whether the file is formatted or not is determined by looking at the
                 extension a filepath is given and by whether the stream is a byte-stream
@@ -245,8 +246,11 @@ class CornerpointGrid:
         return cls(coord, zcorn, map_axes)
 
     def find_cell_containing_point(
-        self, points: npt.ArrayLike, map_coordinates: bool = True
-    ) -> list[tuple[float, float, float] | None]:
+        self,
+        points: npt.ArrayLike,
+        map_coordinates: bool = True,
+        tolerance: float = 1.0e-6,
+    ) -> list[tuple[int, int, int] | None]:
         """Find a cell in the grid which contains the given point.
 
         Args:
@@ -255,13 +259,16 @@ class CornerpointGrid:
             map_coordinates:
                 Whether points are in the map coordinate system.
                 Defaults to True.
+            tolerance:
+                The maximum distance to the cell boundary a point can have to
+                be considered to be contained in the cell.
 
         Returns:
-            list of i,j,k indecies for each point (or None if the
+            list of i,j,k indices for each point (or None if the
             point is not contained in any cell.
         """
         points = np.asarray(points)
-        result: list[tuple[float, float, float] | None] = []
+        result: list[tuple[int, int, int] | None] = []
         if map_coordinates and self.map_axes is not None:
             points = self.map_axes.transform_map_points(points)
 
@@ -321,7 +328,7 @@ class CornerpointGrid:
             def __lt__(self, other: object) -> bool:
                 """Used to order elements in the search queue.
 
-                The Quads are orderd by distance_from_bounds.
+                The Quads are ordered by distance_from_bounds.
                 """
                 if not isinstance(other, Quad):
                     return False
@@ -346,14 +353,16 @@ class CornerpointGrid:
 
                 # If the quad contains the point then search through each k index
                 # for that quad
-                if node.distance_from_bounds <= 0 and Path(vertices).contains_points(
-                    [p[0:2]]
-                ):
+                if node.distance_from_bounds <= tolerance and Path(
+                    vertices
+                ).contains_points([p[0:2]], radius=tolerance):
                     for k in range(self.zcorn.shape[2]):
                         zcorn = self.zcorn[i, j, k]
+                        z = p[2]
                         # Prune by bounding box first then check whether point_in_cell
-                        if zcorn.min() <= p[2] <= zcorn.max() and self.point_in_cell(
-                            p, i, j, k, map_coordinates=False
+                        if (
+                            zcorn.min() - tolerance <= z <= zcorn.max() + tolerance
+                            and self.point_in_cell(p, i, j, k, map_coordinates=False)
                         ):
                             prev_ij = (i, j)
                             result.append((i, j, k))
@@ -378,6 +387,30 @@ class CornerpointGrid:
 
         return result
 
+    def cell_corners(self, i: int, j: int, k: int) -> npt.NDArray[np.float32]:
+        """Array of coordinates for all corners of the cell at i,j,k
+
+        The order of the corners are the same as in zcorn.
+        """
+        pillar_vertices = np.concatenate(
+            [
+                self.coord[i, j, :],
+                self.coord[i, j + 1, :],
+                self.coord[i + 1, j, :],
+                self.coord[i + 1, j + 1, :],
+            ]
+        )
+        top = pillar_vertices[::2][[0, 2, 1, 3]]
+        bot = pillar_vertices[1::2][[0, 2, 1, 3]]
+        top_z = top[:, 2]
+        bot_z = bot[:, 2]
+
+        def twice(a: npt.NDArray[Any]) -> npt.NDArray[Any]:
+            return np.concatenate([a, a])
+
+        t = (self.zcorn[i, j, k] - twice(top_z)) / twice(bot_z - top_z)
+        return twice(top) + t[:, np.newaxis] * twice(bot - top)
+
     def point_in_cell(
         self,
         points: npt.ArrayLike,
@@ -389,12 +422,14 @@ class CornerpointGrid:
     ) -> npt.NDArray[np.bool_]:
         """Whether the points (x,y,z) is in the cell at (i,j,k).
 
+        For containment the cell are considered to have bilinear faces.
+
         Param:
             points:
                 x,y,z triple or array of x,y,z triples to be tested for containment.
             tolerance:
-                The maximum distance to the cell boundary a point can have to
-                be considered to be contained in the cell.
+                The tolerance used for numerical precision in the linear
+                interpolation calculation.
             map_coordinates:
                 Whether the given points are in the mapaxes coordinate system,
                 defaults to true.
@@ -408,43 +443,65 @@ class CornerpointGrid:
             points = points[np.newaxis, :]
         if map_coordinates and self.map_axes is not None:
             points = self.map_axes.transform_map_points(points)
-        pillar_vertices = np.concatenate(
+
+        vertices = self.cell_corners(i, j, k).astype(np.float64)
+
+        corner_signs = np.array(
             [
-                self.coord[i, j, :],
-                self.coord[i, j + 1, :],
-                self.coord[i + 1, j, :],
-                self.coord[i + 1, j + 1, :],
+                [-1, -1, -1],
+                [1, -1, -1],
+                [-1, 1, -1],
+                [1, 1, -1],
+                [-1, -1, 1],
+                [1, -1, 1],
+                [-1, 1, 1],
+                [1, 1, 1],
             ]
         )
-        top = pillar_vertices[::2][[0, 2, 1, 3]]
-        bot = pillar_vertices[1::2][[0, 2, 1, 3]]
-        top_z = top[:, 2]
-        bot_z = bot[:, 2]
-
-        def twice(a: npt.NDArray[Any]) -> npt.NDArray[Any]:
-            return np.concatenate([a, a])
 
-        t = (self.zcorn[i, j, k] - twice(top_z)) / twice(bot_z - top_z)
-        mesh = trimesh.Trimesh(
-            vertices=twice(top) + t[:, np.newaxis] * twice(bot - top),
-            faces=np.array(
-                [
-                    [0, 1, 2],
-                    [1, 2, 3],
-                    [0, 1, 5],
-                    [0, 4, 5],
-                    [0, 2, 6],
-                    [0, 4, 6],
-                    [4, 6, 5],
-                    [5, 6, 7],
-                    [1, 3, 7],
-                    [1, 5, 7],
-                    [2, 3, 7],
-                    [2, 3, 6],
-                ]
-            ),
-        )
-        return mesh.contains(points) | (mesh.nearest.on_surface(points)[1] < tolerance)
+        def residual(
+            point: tuple[float, float, float],
+        ) -> Callable[[npt.NDArray[np.float64]], npt.NDArray[np.float64]]:
+            def inner(
+                xi_eta_zeta: npt.NDArray[np.float64],
+            ) -> npt.NDArray[np.float64]:
+                xi, eta, zeta = xi_eta_zeta
+                shape_matrix = (
+                    1
+                    / 8
+                    * (1 + xi * corner_signs[:, 0])
+                    * (1 + eta * corner_signs[:, 1])
+                    * (1 + zeta * corner_signs[:, 2])
+                )
+                mapped = shape_matrix @ vertices
+                return mapped - point
+
+            return inner
+
+        solutions = []
+        for point in points:
+            point = point.astype(np.float64)
+            initial_guess = 2 * (point - vertices[0]) / (vertices[6] - vertices[0]) - 1
+            initial_guess = np.clip(initial_guess, -1, 1)
+            np.nan_to_num(initial_guess, copy=False)
+            sol = scipy.optimize.least_squares(
+                residual(point),
+                initial_guess,
+                method="trf",
+                xtol=tolerance,
+                ftol=tolerance,
+                gtol=tolerance,
+            )
+            if not sol.success:
+                solutions.append(False)
+            else:
+                solutions.append(
+                    bool(
+                        np.all(np.abs(sol.x) <= 1.0 + tolerance)
+                        and np.linalg.norm(residual(point)(sol.x)) <= 1e-4 + tolerance
+                    )
+                )
+        return np.array(solutions, dtype=np.bool_)
 
     def _pillars_z_plane_intersection(self, z: np.float32) -> npt.NDArray[np.float32]:
         shape = self.coord.shape

{resfo_utilities-0.0.1.dist-info → resfo_utilities-0.0.3.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: resfo-utilities
-Version: 0.0.1
+Version: 0.0.3
 Summary: A utility library for working with the output of reservoir simulators.
 Author-email: Equinor <fg_sib-scout@equinor.com>
 Maintainer-email: Eivind Jahren <ejah@equinor.com>, Håkon Steinkopf Søhoel <hsoho@equinor.com>
@@ -16,11 +16,11 @@ Classifier: Programming Language :: Python :: 3.12
 Classifier: Programming Language :: Python :: 3.13
 Requires-Python: <3.14,>=3.11
 Description-Content-Type: text/markdown
+License-File: LICENSE.md
 Requires-Dist: numpy
 Requires-Dist: resfo
-Requires-Dist: shapely
-Requires-Dist: trimesh[easy]
 Requires-Dist: matplotlib
+Requires-Dist: scipy
 Provides-Extra: doc
 Requires-Dist: sphinx; extra == "doc"
 Requires-Dist: sphinx-rtd-theme; extra == "doc"
@@ -29,11 +29,12 @@ Requires-Dist: pytest; extra == "dev"
 Requires-Dist: hypothesis; extra == "dev"
 Requires-Dist: pre-commit; extra == "dev"
 Requires-Dist: mypy; extra == "dev"
-Requires-Dist: types-shapely; extra == "dev"
 Requires-Dist: pytest-benchmark; extra == "dev"
+Requires-Dist: scipy-stubs; extra == "dev"
+Dynamic: license-file
 
-resfo
-===========
+resfo-utilities
+===============
 
 
 resfo-utilities is a library for working with output from

resfo_utilities-0.0.3.dist-info/RECORD

@@ -0,0 +1,7 @@
+resfo_utilities/__init__.py,sha256=_O7IbN2VxBuoWsSeVlQl6LSi_N0Tnb1YAOwiPNcy2i0,146
+resfo_utilities/_cornerpoint_grid.py,sha256=ZJleszWHKEeVyIsW0If3H3OWX64Tjdg_tgo-etlenA0,19905
+resfo_utilities-0.0.3.dist-info/licenses/LICENSE.md,sha256=3IXI3x1RN4jDR2PonpWF1guc33zagcTgpq_VnboE3UU,7653
+resfo_utilities-0.0.3.dist-info/METADATA,sha256=gRqzsGS6p87TNZQ6G57WI5exXkF4ICAwATdLN3ulUtk,2356
+resfo_utilities-0.0.3.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+resfo_utilities-0.0.3.dist-info/top_level.txt,sha256=VjItoaJHqsDLhHEvCjEI5bN2sZy55tA-zlkl-CtggEU,16
+resfo_utilities-0.0.3.dist-info/RECORD,,

resfo_utilities-0.0.3.dist-info/licenses/LICENSE.md

@@ -0,0 +1,166 @@
+
+                   GNU LESSER GENERAL PUBLIC LICENSE
+                       Version 3, 29 June 2007
+
+ Copyright (C) 2007 Free Software Foundation, Inc. <https://fsf.org/>
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+
+  This version of the GNU Lesser General Public License incorporates
+the terms and conditions of version 3 of the GNU General Public
+License, supplemented by the additional permissions listed below.
+
+  0. Additional Definitions.
+
+  As used herein, "this License" refers to version 3 of the GNU Lesser
+General Public License, and the "GNU GPL" refers to version 3 of the GNU
+General Public License.
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+other than an Application or a Combined Work as defined below.
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resfo_utilities-0.0.1.dist-info/RECORD

@@ -1,6 +0,0 @@
-resfo_utilities/__init__.py,sha256=_O7IbN2VxBuoWsSeVlQl6LSi_N0Tnb1YAOwiPNcy2i0,146
-resfo_utilities/_cornerpoint_grid.py,sha256=yZjPVyctdo9fqXmRjFBCtwmC6whEdokKLHB5FqCnosI,17893
-resfo_utilities-0.0.1.dist-info/METADATA,sha256=d1osGa2k453dePtqlXueGF8y8E_AM_qvgPF9O1W3cf0,2328
-resfo_utilities-0.0.1.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-resfo_utilities-0.0.1.dist-info/top_level.txt,sha256=VjItoaJHqsDLhHEvCjEI5bN2sZy55tA-zlkl-CtggEU,16
-resfo_utilities-0.0.1.dist-info/RECORD,,