resfo-utilities 0.0.2__tar.gz → 0.0.3__tar.gz

{resfo_utilities-0.0.2 → resfo_utilities-0.0.3}/.github/workflows/testing.yml

@@ -22,11 +22,11 @@ jobs:
         python-version: ["3.11", "3.12", "3.13"]
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
       - uses: actions/setup-python@v6
         with:
           python-version: ${{ matrix.python-version }}
-      - uses: astral-sh/setup-uv@v6
+      - uses: astral-sh/setup-uv@v7
         with:
           enable-cache: true
           python-version: ${{ matrix.python-version }}

{resfo_utilities-0.0.2 → resfo_utilities-0.0.3}/.github/workflows/typing.yml

@@ -29,7 +29,7 @@ jobs:
         python-version: "3.13"
 
     - name: Install uv
-      uses: astral-sh/setup-uv@v6
+      uses: astral-sh/setup-uv@v7
       with:
         enable-cache: true
         python-version: "3.13"

resfo_utilities-0.0.3/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.
+
+  "The Library" refers to a covered work governed by this License,
+other than an Application or a Combined Work as defined below.
+
+  An "Application" is any work that makes use of an interface provided
+by the Library, but which is not otherwise based on the Library.
+Defining a subclass of a class defined by the Library is deemed a mode
+of using an interface provided by the Library.
+
+  A "Combined Work" is a work produced by combining or linking an
+Application with the Library.  The particular version of the Library
+with which the Combined Work was made is also called the "Linked
+Version".
+
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+Corresponding Source for the Combined Work, excluding any source code
+for portions of the Combined Work that, considered in isolation, are
+based on the Application, and not on the Linked Version.
+
+  The "Corresponding Application Code" for a Combined Work means the
+object code and/or source code for the Application, including any data
+and utility programs needed for reproducing the Combined Work from the
+Application, but excluding the System Libraries of the Combined Work.
+
+  1. Exception to Section 3 of the GNU GPL.
+
+  You may convey a covered work under sections 3 and 4 of this License
+without being bound by section 3 of the GNU GPL.
+
+  2. Conveying Modified Versions.
+
+  If you modify a copy of the Library, and, in your modifications, a
+facility refers to a function or data to be supplied by an Application
+that uses the facility (other than as an argument passed when the
+facility is invoked), then you may convey a copy of the modified
+version:
+
+   a) under this License, provided that you make a good faith effort to
+   ensure that, in the event an Application does not supply the
+   function or data, the facility still operates, and performs
+   whatever part of its purpose remains meaningful, or
+
+   b) under the GNU GPL, with none of the additional permissions of
+   this License applicable to that copy.
+
+  3. Object Code Incorporating Material from Library Header Files.
+
+  The object code form of an Application may incorporate material from
+a header file that is part of the Library.  You may convey such object
+code under terms of your choice, provided that, if the incorporated
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+(ten or fewer lines in length), you do both of the following:
+
+   a) Give prominent notice with each copy of the object code that the
+   Library is used in it and that the Library and its use are
+   covered by this License.
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+  4. Combined Works.
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+   copies of the GNU GPL and this license document.
+
+   d) Do one of the following:
+
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+       suitable for, and under terms that permit, the user to
+       recombine or relink the Application with a modified version of
+       the Linked Version to produce a modified Combined Work, in the
+       manner specified by section 6 of the GNU GPL for conveying
+       Corresponding Source.
+
+       1) Use a suitable shared library mechanism for linking with the
+       Library.  A suitable mechanism is one that (a) uses at run time
+       a copy of the Library already present on the user's computer
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+   e) Provide Installation Information, but only if you would otherwise
+   be required to provide such information under section 6 of the
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+   Application with a modified version of the Linked Version. (If
+   you use option 4d0, the Installation Information must accompany
+   the Minimal Corresponding Source and Corresponding Application
+   Code. If you use option 4d1, you must provide the Installation
+   Information in the manner specified by section 6 of the GNU GPL
+   for conveying Corresponding Source.)
+
+  5. Combined Libraries.
+
+  You may place library facilities that are a work based on the
+Library side by side in a single library together with other library
+facilities that are not Applications and are not covered by this
+License, and convey such a combined library under terms of your
+choice, if you do both of the following:
+
+   a) Accompany the combined library with a copy of the same work based
+   on the Library, uncombined with any other library facilities,
+   conveyed under the terms of this License.
+
+   b) Give prominent notice with the combined library that part of it
+   is a work based on the Library, and explaining where to find the
+   accompanying uncombined form of the same work.
+
+  6. Revised Versions of the GNU Lesser General Public License.
+
+  The Free Software Foundation may publish revised and/or new versions
+of the GNU Lesser General Public License from time to time. Such new
+versions will be similar in spirit to the present version, but may
+differ in detail to address new problems or concerns.
+
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+Library as you received it specifies that a certain numbered version
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+published by the Free Software Foundation. If the Library as you
+received it does not specify a version number of the GNU Lesser
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+
+  If the Library as you received it specifies that a proxy can decide
+whether future versions of the GNU Lesser General Public License shall
+apply, that proxy's public statement of acceptance of any version is
+permanent authorization for you to choose that version for the
+Library.

{resfo_utilities-0.0.2 → resfo_utilities-0.0.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: resfo-utilities
-Version: 0.0.2
+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-0.0.2 → resfo_utilities-0.0.3}/README.md

@@ -1,5 +1,5 @@
-resfo
-===========
+resfo-utilities
+===============
 
 
 resfo-utilities is a library for working with output from

{resfo_utilities-0.0.2 → resfo_utilities-0.0.3}/docs/source/glossary.rst

@@ -4,14 +4,14 @@ Glossary
 .. glossary::
 
     corner-point grid
-        A corner-point grid is a tessellation of a 3D volumne where
+        A corner-point grid is a tessellation of a 3D volume where
         each cell is a hexahedron. See the `corner-point grid wikipedia page`_  or
         `OPM Flow manual`_ section 6.2.2 for more information.
 
     pillar
         In a :term:`corner-point grid` the pillars are a set of straight lines used
-        to define each cell. The 8 corner vertecies of each cell is determined by
-        the giving the height along four adjecent pillars.
+        to define each cell. The 8 corner vertices of each cell is determined by
+        giving the height along four adjacent pillars.
 
     UTM-coordinates
         The Universal Transverse Mercator (UTM) is a coordinate system based on

{resfo_utilities-0.0.2 → resfo_utilities-0.0.3}/pyproject.toml

@@ -15,7 +15,7 @@ classifiers=[
     "Programming Language :: Python :: 3.12",
     "Programming Language :: Python :: 3.13",
 ]
-dependencies = ["numpy","resfo", "shapely", "trimesh[easy]", "matplotlib"]
+dependencies = ["numpy","resfo", "matplotlib", "scipy"]
 dynamic=["version"]
 
 authors = [
@@ -45,8 +45,8 @@ dev = [
     "hypothesis",
     "pre-commit",
     "mypy",
-    "types-shapely",
     "pytest-benchmark",
+    "scipy-stubs",
 ]
 
 [tool.setuptools_scm]

{resfo_utilities-0.0.2 → resfo_utilities-0.0.3}/src/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, 6, 7],
-                ]
-            ),
-        )
-        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-0.0.2 → resfo_utilities-0.0.3}/src/resfo_utilities.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: resfo-utilities
-Version: 0.0.2
+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-0.0.2 → resfo_utilities-0.0.3}/src/resfo_utilities.egg-info/SOURCES.txt

@@ -3,6 +3,7 @@
 .pre-commit-config.yaml
 .readthedocs.yaml
 CONTRIBUTING.md
+LICENSE.md
 README.md
 SECURITY.md
 pyproject.toml

{resfo_utilities-0.0.2 → resfo_utilities-0.0.3}/src/resfo_utilities.egg-info/requires.txt

@@ -1,16 +1,15 @@
 numpy
 resfo
-shapely
-trimesh[easy]
 matplotlib
+scipy
 
 [dev]
 pytest
 hypothesis
 pre-commit
 mypy
-types-shapely
 pytest-benchmark
+scipy-stubs
 
 [doc]
 sphinx

{resfo_utilities-0.0.2 → resfo_utilities-0.0.3}/tests/performance/test_find_cell_performance.py

@@ -7,7 +7,7 @@ import pytest
 @pytest.fixture
 def large_regular_grid():
     ni, nj, nk = 50, 50, 10
-    height = 500
+    height = 100
     top_depth = 0.0
     bot_depth = top_depth + height
     coord = np.zeros((ni + 1, nj + 1, 2, 3), dtype=np.float32)
@@ -16,14 +16,14 @@ def large_regular_grid():
         coord[i, j, 0] = [i, j, top_depth]
         coord[i, j, 1] = [i, j, bot_depth]
     for i, j, k in product(range(ni), range(nj), range(nk)):
-        zcorn[i, j, k] = [height * (k // nk)] * 4 + [height * ((k + 1) // nk)] * 4
+        zcorn[i, j, k] = [height * (k / nk)] * 4 + [height * ((k + 1) / nk)] * 4
     return CornerpointGrid(coord, zcorn)
 
 
 def test_benchmark_find_cell(large_regular_grid, benchmark):
     def run():
         assert large_regular_grid.find_cell_containing_point(
-            [(i + 25.5, j + 25.5, 20.0) for i, j in product(range(10), range(10))]
-        ) == [(i + 25, j + 25, 9) for i, j in product(range(10), range(10))]
+            [(i + 25.5, j + 25.5, 20.5) for i, j in product(range(10), range(10))]
+        ) == [(i + 25, j + 25, 2) for i, j in product(range(10), range(10))]
 
     benchmark(run)