capytaine 2.3__cp312-cp312-macosx_14_0_arm64.whl → 3.0.0a1__cp312-cp312-macosx_14_0_arm64.whl

capytaine/io/xarray.py

@@ -11,6 +11,7 @@ from datetime import datetime
 from itertools import product
 from collections import Counter
 from typing import Sequence, List, Union
+from pathlib import Path
 
 import numpy as np
 import pandas as pd
@@ -18,6 +19,7 @@ import xarray as xr
 
 from capytaine import __version__
 from capytaine.bodies.bodies import FloatingBody
+from capytaine.bodies.multibodies import Multibody
 from capytaine.bem.problems_and_results import (
     LinearPotentialFlowProblem, DiffractionProblem, RadiationProblem,
     LinearPotentialFlowResult, _default_parameters)
@@ -43,7 +45,7 @@ def _unsqueeze_dimensions(data_array, dimensions=None):
 
 
 def problems_from_dataset(dataset: xr.Dataset,
-                          bodies: Union[FloatingBody, Sequence[FloatingBody]],
+                          bodies: Union[FloatingBody, Sequence[FloatingBody], Multibody, Sequence[Multibody]],
                           ) -> List[LinearPotentialFlowProblem]:
     """Generate a list of problems from a test matrix.
 
@@ -64,7 +66,7 @@ def problems_from_dataset(dataset: xr.Dataset,
     ValueError
         if required fields are missing in the dataset
     """
-    if isinstance(bodies, FloatingBody):
+    if isinstance(bodies, (FloatingBody, Multibody)):
         bodies = [bodies]
 
     # Should be done before looking for `frequency_keys`, otherwise
@@ -257,7 +259,7 @@ def hydrostatics_dataset(bodies: Sequence[FloatingBody]) -> xr.Dataset:
         if len(bodies_properties) > 0:
             bodies_properties = xr.concat(bodies_properties.values(), pd.Index(bodies_properties.keys(), name='body_name'))
             bodies_properties = _squeeze_dimensions(bodies_properties, dimensions=['body_name'])
-            dataset = xr.merge([dataset, {body_property: bodies_properties}])
+            dataset = xr.merge([dataset, {body_property: bodies_properties}], compat="no_conflicts", join="outer")
     return dataset
 
 
@@ -279,22 +281,24 @@ def kochin_data_array(results: Sequence[LinearPotentialFlowResult],
                                  compute_kochin(result, theta_range, **kwargs))
     ])
 
+    main_freq_type = Counter((res.provided_freq_type for res in results)).most_common(1)[0][0]
+
     kochin_data = xr.Dataset()
 
     if "RadiationResult" in set(records['kind']):
         radiation = _dataset_from_dataframe(
             records[records['kind'] == "RadiationResult"],
             variables=['kochin'],
-            dimensions=['omega', 'radiating_dof', 'theta'],
+            dimensions=[main_freq_type, 'radiating_dof', 'theta'],
             optional_dims=['g', 'rho', 'body_name', 'water_depth', 'forward_speed', 'wave_direction']
         )
-        kochin_data['kochin'] = radiation['kochin']
+        kochin_data['kochin_radiation'] = radiation['kochin']
 
     if "DiffractionResult" in set(records['kind']):
         diffraction = _dataset_from_dataframe(
             records[records['kind'] == "DiffractionResult"],
             ['kochin'],
-            dimensions=['omega', 'wave_direction', 'theta'],
+            dimensions=[main_freq_type, 'wave_direction', 'theta'],
             optional_dims=['g', 'rho', 'body_name', 'water_depth', 'forward_speed']
         )
         kochin_data['kochin_diffraction'] = diffraction['kochin']
@@ -416,7 +420,7 @@ def assemble_dataset(results,
             variables=['added_mass', 'radiation_damping'],
             dimensions=[main_freq_type, 'radiating_dof', 'influenced_dof'],
             optional_dims=optional_dims + ['wave_direction'])
-        dataset = xr.merge([dataset, radiation_cases])
+        dataset = xr.merge([dataset, radiation_cases], compat="no_conflicts", join="outer")
 
     # DIFFRACTION RESULTS
     if "DiffractionResult" in kinds_of_results:
@@ -425,7 +429,7 @@ def assemble_dataset(results,
             variables=['diffraction_force', 'Froude_Krylov_force'],
             dimensions=[main_freq_type, 'wave_direction', 'influenced_dof'],
             optional_dims=optional_dims)
-        dataset = xr.merge([dataset, diffraction_cases])
+        dataset = xr.merge([dataset, diffraction_cases], compat="no_conflicts", join="outer")
         dataset['excitation_force'] = dataset['Froude_Krylov_force'] + dataset['diffraction_force']
 
     # OTHER FREQUENCIES TYPES
@@ -519,7 +523,7 @@ def assemble_dataset(results,
             LOG.warning('Bemio data import being used, hydrostatics=True is ignored.')
         else:
             bodies = list({result.body for result in results})
-            dataset = xr.merge([dataset, hydrostatics_dataset(bodies)])
+            dataset = xr.merge([dataset, hydrostatics_dataset(bodies)], compat="no_conflicts", join="outer")
 
     for var in set(dataset) | set(dataset.coords):
         if var in VARIABLES_ATTRIBUTES:
@@ -532,7 +536,7 @@ def assemble_dataset(results,
 
 def assemble_matrices(results):
     """Simplified version of assemble_dataset, returning only bare matrices.
-    Meant mainly for teaching without introducing Xarray to beginers.
+    Meant mainly for teaching without introducing Xarray to beginners.
 
     Parameters
     ----------
@@ -662,6 +666,7 @@ def export_dataset(filename, dataset, format=None, **kwargs):
             (format is not None and format.lower() == "nemoh")
             ):
         from capytaine.io.legacy import write_dataset_as_tecplot_files
+        Path(filename).mkdir(exist_ok=True)
         write_dataset_as_tecplot_files(filename, dataset, **kwargs)
     else:
         raise ValueError("`export_dataset` could not infer export format based on filename or `format` argument.\n"

capytaine/meshes/__init__.py

@@ -1,6 +1,2 @@
-# Copyright (C) 2017-2019 Matthieu Ancellin, based on the work of François Rongère
-# See LICENSE file at <https://github.com/mancellin/capytaine>
-
-from capytaine.meshes.meshes import Mesh
-from capytaine.meshes.collections import CollectionOfMeshes
-from capytaine.meshes.symmetric import ReflectionSymmetricMesh, TranslationalSymmetricMesh, AxialSymmetricMesh
+from .meshes import Mesh
+from .symmetric_meshes import ReflectionSymmetricMesh, RotationSymmetricMesh

capytaine/meshes/abstract_meshes.py

@@ -0,0 +1,375 @@
+# Copyright 2025 Mews Labs
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+from __future__ import annotations
+
+import logging
+from abc import ABC, abstractmethod
+from functools import cached_property, lru_cache
+from typing import Literal, Tuple
+
+import numpy as np
+
+from capytaine.meshes.surface_integrals import SurfaceIntegralsMixin
+from capytaine.tools.deprecation_handling import _get_water_depth
+from capytaine.meshes.geometry import connected_components, connected_components_of_waterline
+
+LOG = logging.getLogger(__name__)
+
+class AbstractMesh(SurfaceIntegralsMixin, ABC):
+    @property
+    @abstractmethod
+    def nb_vertices(self) -> int:
+        ...
+
+    @property
+    @abstractmethod
+    def nb_faces(self) -> int:
+        ...
+
+    @property
+    @abstractmethod
+    def faces_normals(self) -> np.ndarray:
+        ...
+
+    @property
+    @abstractmethod
+    def faces_areas(self) -> np.ndarray:
+        ...
+
+    @property
+    @abstractmethod
+    def faces_centers(self) -> np.ndarray:
+        ...
+
+    @property
+    @abstractmethod
+    def faces_radiuses(self) -> np.ndarray:
+        ...
+
+    @property
+    @abstractmethod
+    def faces(self) -> np.ndarray:
+        ...
+
+    @property
+    @abstractmethod
+    def quadrature_points(self) -> np.ndarray:
+        ...
+
+    @cached_property
+    def z_span(self) -> Tuple[float, float]:
+        return (self.vertices[:, 2].min(), self.vertices[:, 2].max())
+
+    @abstractmethod
+    def __str__(self) -> str:
+        ...
+
+    @abstractmethod
+    def __short_str__(self) -> str:
+        ...
+
+    @abstractmethod
+    def with_quadrature(self, quadrature_method):
+        ...
+
+    @abstractmethod
+    def extract_faces(self, faces_id, *, name=None) -> AbstractMesh:
+        ...
+
+    @abstractmethod
+    def translated(self, shift, *, name=None) -> AbstractMesh:
+        ...
+
+    def translated_x(self, dx: float, *, name=None) -> AbstractMesh:
+        """Return a new Mesh translated in the x-direction along `dx`."""
+        return self.translated([dx, 0.0, 0.0], name=name)
+
+    def translated_y(self, dy: float, *, name=None) -> AbstractMesh:
+        """Return a new Mesh translated in the y-direction along `dy`."""
+        return self.translated([0.0, dy, 0.0], name=name)
+
+    def translated_z(self, dz: float, *, name=None) -> AbstractMesh:
+        """Return a new Mesh translated in the z-direction along `dz`."""
+        return self.translated([0.0, 0.0, dz], name=name)
+
+    @abstractmethod
+    def rotated_with_matrix(self, R, *, name=None) -> AbstractMesh:
+        ...
+
+    def rotated_x(self, angle: float, *, name=None) -> AbstractMesh:
+        """Return a new Mesh rotated around the x-axis using the provided rotation angle in radians"""
+        c, s = np.cos(angle), np.sin(angle)
+        R = np.array([[1, 0, 0], [0, c, -s], [0, s, c]])
+        return self.rotated_with_matrix(R, name=name)
+
+    def rotated_y(self, angle: float, *, name=None) -> AbstractMesh:
+        """Return a new Mesh rotated around the y-axis using the provided rotation angle in radians"""
+        c, s = np.cos(angle), np.sin(angle)
+        R = np.array([[c, 0, s], [0, 1, 0], [-s, 0, c]])
+        return self.rotated_with_matrix(R, name=name)
+
+    def rotated_z(self, angle: float, *, name=None) -> AbstractMesh:
+        """Return a new Mesh rotated around the z-axis using the provided rotation angle in radians"""
+        c, s = np.cos(angle), np.sin(angle)
+        R = np.array([[c, -s, 0], [s, c, 0], [0, 0, 1]])
+        return self.rotated_with_matrix(R, name=name)
+
+    def rotated_such_that_vectors_are_aligned(self, a, b, *, eps=1e-8, name=None) -> AbstractMesh:
+        a = np.asarray(a, dtype=float)
+        b = np.asarray(b, dtype=float)
+
+        # Normalize input vectors
+        a_norm = np.linalg.norm(a)
+        b_norm = np.linalg.norm(b)
+        if a_norm < eps or b_norm < eps:
+            raise ValueError("Input vectors must be non-zero")
+
+        a_hat = a / a_norm
+        b_hat = b / b_norm
+
+        # Cross and dot products
+        v = np.cross(a_hat, b_hat)
+        c = np.dot(a_hat, b_hat)
+        s = np.linalg.norm(v)
+
+        # Case 1: vectors are already aligned
+        if s < eps and c > 0:
+            return self.copy(name=name)
+
+        # Case 2: vectors are opposite
+        if s < eps and c < 0:
+            # Find an arbitrary orthogonal vector
+            # Prefer axis least aligned with a_hat
+            axis = np.array([1.0, 0.0, 0.0])
+            if abs(a_hat[0]) > abs(a_hat[1]):
+                axis = np.array([0.0, 1.0, 0.0])
+            axis = axis - a_hat * np.dot(a_hat, axis)
+            axis /= np.linalg.norm(axis)
+
+            # Rotation by pi around axis
+            K = np.array([[0, -axis[2], axis[1]],
+                          [axis[2], 0, -axis[0]],
+                          [-axis[1], axis[0], 0]])
+            return self.rotated_with_matrix(np.eye(3) + 2 * K @ K, name=name)
+
+        # General case: Rodrigues' rotation formula
+        K = np.array([[0, -v[2], v[1]],
+                      [v[2], 0, -v[0]],
+                      [-v[1], v[0], 0]])
+
+        R = np.eye(3) + K + K @ K * ((1 - c) / (s ** 2))
+        return self.rotated_with_matrix(R, name=name)
+
+    def mirrored(self, plane: Literal['xOz', 'yOz'], *, name=None) -> AbstractMesh:
+        ...
+
+    @abstractmethod
+    def join_meshes(*meshes, return_masks=False, name=None) -> AbstractMesh:
+        ...
+
+    def _common_metadata_keys(*meshes):
+        metadata_keys = [set(m.faces_metadata.keys()) for m in meshes]
+        common_metadata_keys = set.intersection(*metadata_keys)
+        lost_metadata_keys = set.union(*metadata_keys) - common_metadata_keys
+        if len(lost_metadata_keys) > 0:
+            LOG.warning(f'The following metadata have been dropped when joining meshes: {lost_metadata_keys}')
+        return common_metadata_keys
+
+    def __add__(self, other: AbstractMesh) -> AbstractMesh:
+        """Combine two meshes using the + operator.
+
+        Parameters
+        ----------
+        other : Mesh
+            Another mesh to combine with this one.
+
+        Returns
+        -------
+        Mesh
+            New mesh containing vertices and faces from both meshes.
+        """
+        if self.name is not None or other.name is not None:
+            name = f"{self.name}+{other.name}"
+        else:
+            name = None
+        return self.join_meshes(other, name=name)
+
+    def lowest_lid_position(self, omega_max, *, g=9.81):
+        z_lid = 0.0
+        for comp in connected_components(self):
+            for ccomp in connected_components_of_waterline(comp):
+                x_span = ccomp.vertices[:, 0].max() - ccomp.vertices[:, 0].min()
+                y_span = ccomp.vertices[:, 1].max() - ccomp.vertices[:, 1].min()
+                p = np.hypot(1/x_span, 1/y_span)
+                z_lid_comp = -np.arctanh(np.pi*g*p/omega_max**2) / (np.pi * p)
+                z_lid = min(z_lid, z_lid_comp)
+        return 0.9*z_lid  # Add a small safety margin
+
+    @abstractmethod
+    def generate_lid(self, z=0.0, faces_max_radius=None, name=None):
+        ...
+
+    @abstractmethod
+    def extract_lid(self, z=0.0):
+        ...
+
+    @abstractmethod
+    def with_normal_vector_going_down(self, **kwargs) -> AbstractMesh:
+        ...
+
+    @abstractmethod
+    def copy(self) -> AbstractMesh:
+        ...
+
+    def with_metadata(self, **new_metadata) -> AbstractMesh:
+        faces_metadata = self.faces_metadata.copy()
+        for k, v in new_metadata.items():
+            faces_metadata[k] = v
+        return self.copy(faces_metadata=faces_metadata)
+
+    def pop_metadata(self, metadata_name) -> Tuple[AbstractMesh, np.ndarray]:
+        faces_metadata = self.faces_metadata.copy()
+        data = faces_metadata.pop(metadata_name)
+        return self.copy(faces_metadata=faces_metadata), data
+
+    def without_metadata(self, *metadata_names) -> AbstractMesh:
+        faces_metadata = self.faces_metadata.copy()
+        for k in metadata_names:
+            del faces_metadata[k]
+        return self.copy(faces_metadata=faces_metadata)
+
+    def without_any_metadata(self) -> AbstractMesh:
+        return self.copy(faces_metadata={})
+
+    @abstractmethod
+    def merged(self) -> AbstractMesh:
+        ...
+
+    @abstractmethod
+    def clipped(self, *, origin, normal, name=None) -> AbstractMesh:
+        ...
+
+    def extract_wedge(self, n: int, axis: str = "z") -> AbstractMesh:
+        """Extract a wedge (angular sector) from the mesh for rotational symmetry.
+
+        Extracts a 1/n sector of the mesh by clipping at angular boundaries.
+        This creates proper faces at the wedge boundaries for clean reconstruction.
+
+        Parameters
+        ----------
+        n : int
+            The rotation order. The wedge will span 360/n degrees.
+        axis : str, optional
+            Only "z" is currently supported.
+
+        Returns
+        -------
+        Mesh
+            A new mesh containing the wedge sector with proper boundary faces.
+
+        Examples
+        --------
+        Extract 1/3 of a sphere (120-degree wedge):
+
+        >>> sphere = mesh_sphere(radius=1.0, resolution=(12, 12))
+        >>> wedge = sphere.extract_wedge(n=3)
+        >>> wedge.nb_faces  # Approximately 1/3 of sphere.nb_faces
+        """
+        if axis != "z":
+            raise NotImplementedError(
+                f"Only 'z' axis is currently supported, got '{axis}'"
+            )
+        if n < 2:
+            raise ValueError(f"Rotation order must be >= 2, got {n}")
+
+        # Wedge angle in radians
+        wedge_angle = 2 * np.pi / n
+
+        # First clip: keep the half with y >= 0 (theta in [0, pi])
+        # This corresponds to the plane y=0, keeping positive y side
+        origin = np.array([0.0, 0.0, 0.0])
+        normal_1 = np.array([0.0, -1.0, 0.0])  # Keep y >= 0
+        wedge = self.clipped(origin=origin, normal=normal_1)
+
+        # Second clip: create the wedge boundary at angle = wedge_angle
+        # The plane passes through the z-axis and has a normal perpendicular to the boundary
+        # For a wedge from theta=0 to theta=wedge_angle, we need to keep theta <= wedge_angle
+        # Normal vector points outward from the wedge (to reject the side we don't want)
+        # At angle theta, the outward normal is [-sin(theta), cos(theta), 0]
+        normal_2 = np.array([-np.sin(wedge_angle), np.cos(wedge_angle), 0.0])
+        wedge = wedge.clipped(origin=origin, normal=normal_2, name=f"{self.name}_wedge_n{n}")
+
+        return wedge
+
+    @lru_cache
+    def immersed_part(self, free_surface=0.0, *, sea_bottom=None, water_depth=None) -> AbstractMesh:
+        """
+        Clip the mesh to keep only the part below the free surface.
+
+        Parameters
+        ----------
+        free_surface: float
+            The :math:`z` coordinate of the free surface (default: 0.0)
+        water_depth: Optional[float]
+            The water depth, as a positive value (default: infinity)
+
+        Returns
+        -------
+        Mesh
+            A new Mesh instance that has been clipped.
+        """
+        water_depth = _get_water_depth(free_surface, water_depth, sea_bottom,
+                                       default_water_depth=np.inf)
+        if (free_surface - water_depth <= self.z_span[0]
+            and self.z_span[1] <= free_surface):  # Already clipped
+            return self  # Shortcut for performance
+        clipped = self.clipped(origin=(0, 0, 0), normal=(0, 0, 1))
+        if water_depth < np.inf:
+            clipped = clipped.clipped(origin=(0, 0, free_surface-water_depth), normal=(0, 0, -1))
+        return clipped
+
+    @abstractmethod
+    def show(self, *, backend=None, **kwargs):
+        ...
+
+    def show_pyvista(self, **kwargs):
+        """
+        Equivalent to show(backend="pyvista").
+        See also :func:`~capytaine.meshes.visualization.show_pyvista`
+        """
+        return self.show(backend="pyvista", **kwargs)
+
+    def show_matplotlib(self, **kwargs):
+        """
+        Equivalent to show(backend="matplotlib").
+        See also :func:`~capytaine.meshes.visualization.show_matplotlib`
+        """
+        return self.show(backend="matplotlib", **kwargs)
+
+    @abstractmethod
+    def export(self, format, **kwargs):
+        ...
+
+    def export_to_pyvista(self, **kwargs):
+        return self.export(format="pyvista", **kwargs)
+
+    def export_to_xarray(self, **kwargs):
+        return self.export(format="xarray", **kwargs)
+
+    def export_to_meshio(self, **kwargs):
+        return self.export(format="meshio", **kwargs)
+
+    def export_to_trimesh(self, **kwargs):
+        return self.export(format="trimesh", **kwargs)