Merge pull request #425 from adtzlr/mesh-tools-as-methods

Enhance `Mesh`: Mesh tools as methods

CHANGELOG.md

@@ -10,6 +10,8 @@ All notable changes to this project will be documented in this file. The format
 ### Changed
 - Change `einsumt` from an optional to a required dependency.
 - Vectorize implementations of `MultiPointConstraint` and `MultiPointContact` and re-implement both as `scipy.sparse.lil_matrix()`.
+- Rename old `Mesh` to `DiscreteGeometry` and rebase new `Mesh` on `DiscreteGeometry`. 
+- Simplify the usage of explicit mesh-related tools by adding them as methods to `Mesh`, i.e. `mesh.tools.expand(Rectangle())` is equivalent to `Rectangle().expand()`.
 
 ### Fixed
 - Fix `tools.project()` for higher-order quad- and hexahedron elements.

src/felupe/mesh/_convert.py

@@ -27,8 +27,8 @@
 
 import numpy as np
 
+from ._discrete_geometry import DiscreteGeometry
 from ._helpers import mesh_or_data
-from ._mesh import Mesh
 
 
 @mesh_or_data

src/felupe/mesh/_discrete_geometry.py

@@ -0,0 +1,102 @@
+# -*- coding: utf-8 -*-
+"""
+ _______  _______  ___      __   __  _______  _______ 
+|       ||       ||   |    |  | |  ||       ||       |
+|    ___||    ___||   |    |  | |  ||    _  ||    ___|
+|   |___ |   |___ |   |    |  |_|  ||   |_| ||   |___ 
+|    ___||    ___||   |___ |       ||    ___||    ___|
+|   |    |   |___ |       ||       ||   |    |   |___ 
+|___|    |_______||_______||_______||___|    |_______|
+
+This file is part of felupe.
+
+Felupe is free software: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+Felupe is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with Felupe.  If not, see <http://www.gnu.org/licenses/>.
+
+"""
+
+import numpy as np
+
+
+class DiscreteGeometry:
+    """A discrete geometry with points, cells and optional a specified cell type.
+
+    Parameters
+    ----------
+    points : ndarray
+        Point coordinates.
+    cells : ndarray
+        Point-connectivity of cells.
+    cell_type : str or None, optional
+        An optional string in VTK-convention that specifies the cell type (default is None). Necessary when a discrete geometry is saved to a file.
+
+    Attributes
+    ----------
+    points : ndarray
+        Point coordinates.
+    cells : ndarray
+        Point-connectivity of cells.
+    cell_type : str or None
+        A string in VTK-convention that specifies the cell type.
+    npoints : int
+        Amount of points.
+    dim : int
+        Dimension of mesh point coordinates.
+    ndof : int
+        Amount of degrees of freedom.
+    ncells : int
+        Amount of cells.
+    points_with_cells : array
+        Array with points connected to cells.
+    points_without_cells : array
+        Array with points not connected to cells.
+    cells_per_point : array
+        Array which counts connected cells per point. Used for averaging results.
+
+    """
+
+    def __init__(self, points, cells, cell_type=None):
+        self.points = np.array(points)
+        self.cells = np.array(cells)
+        self.cell_type = cell_type
+
+        self.update(self.cells)
+
+    def update(self, cells, cell_type=None):
+        "Update the cell and dimension attributes with a given cell array."
+        self.cells = cells
+
+        if cell_type is not None:
+            self.cell_type = cell_type
+
+        # obtain dimensions
+        self.npoints, self.dim = self.points.shape
+        self.ndof = self.points.size
+        self.ncells = self.cells.shape[0]
+
+        # get number of cells per point
+        points_in_cell, self.cells_per_point = np.unique(cells, return_counts=True)
+
+        # check if there are points without cells
+        if self.npoints != len(self.cells_per_point):
+            self.point_has_cell = np.isin(np.arange(self.npoints), points_in_cell)
+            # update "cells_per_point" ... cells per point
+            cells_per_point = -np.ones(self.npoints, dtype=int)
+            cells_per_point[points_in_cell] = self.cells_per_point
+            self.cells_per_point = cells_per_point
+
+            self.points_without_cells = np.arange(self.npoints)[~self.point_has_cell]
+            self.points_with_cells = np.arange(self.npoints)[self.point_has_cell]
+        else:
+            self.points_without_cells = np.array([], dtype=int)
+            self.points_with_cells = np.arange(self.npoints)

src/felupe/mesh/_helpers.py

@@ -27,12 +27,10 @@
 
 from functools import wraps
 
-from ._mesh import Mesh
-
 
 def mesh_or_data(meshfun):
-    """If a ``Mesh`` is passed to a mesh function, extract ``points`` and
-    ``cells`` arrays along with the ``cell_type`` and return a ``Mesh``
+    """If a ``DiscreteGeometry`` is passed to a mesh function, extract ``points`` and
+    ``cells`` arrays along with the ``cell_type`` and return a ``DiscreteGeometry``
     as a result."""
 
     @wraps(meshfun)
@@ -44,8 +42,8 @@ def mesh_or_points_cells_type(*args, **kwargs):
         # check if unnamed args are passed
         if len(args) > 0:
 
-            # meshfun(Mesh)
-            if isinstance(args[0], Mesh):
+            # meshfun(DiscreteGeometry)
+            if hasattr(args[0], "__mesh__"):
 
                 # set mesh flag
                 is_mesh = True
@@ -55,6 +53,9 @@ def mesh_or_points_cells_type(*args, **kwargs):
                 cells = args[0].cells
                 cell_type = args[0].cell_type
 
+                # get mesh class
+                Mesh = args[0].__mesh__
+
                 # remove Mesh from args
                 args = args[1:]
 
@@ -104,7 +105,7 @@ def mesh_or_points_cells_type(*args, **kwargs):
         # call mesh manipulation function
         points, cells, cell_type = meshfun(points, cells, cell_type, *args, **kwargs)
 
-        # return a Mesh if a Mesh was passed
+        # return a DiscreteGeometry if a DiscreteGeometry was passed
         if is_mesh:
             return Mesh(points=points, cells=cells, cell_type=cell_type)
 

src/felupe/mesh/_mesh.py

@@ -26,11 +26,29 @@
 """
 
 from copy import deepcopy
+from functools import wraps
 
 import numpy as np
 
+from ._convert import (
+    add_midpoints_edges,
+    add_midpoints_faces,
+    add_midpoints_volumes,
+    collect_edges,
+    collect_faces,
+    collect_volumes,
+    convert,
+)
+from ._discrete_geometry import DiscreteGeometry
+from ._tools import expand, mirror, revolve, rotate, runouts, sweep, triangulate
 
-class Mesh:
+
+def as_mesh(obj):
+    "Convert a ``DiscreteGeometry`` object to a ``Mesh`` object."
+    return Mesh(points=obj.points, cells=obj.cells, cell_type=obj.cell_type)
+
+
+class Mesh(DiscreteGeometry):
     """A mesh with points, cells and optional a specified cell type.
 
     Parameters
@@ -50,20 +68,6 @@ class Mesh:
         Point-connectivity of cells.
     cell_type : str or None
         A string in VTK-convention that specifies the cell type.
-    npoints : int
-        Amount of points.
-    dim : int
-        Dimension of mesh point coordinates.
-    ndof : int
-        Amount of degrees of freedom.
-    ncells : int
-        Amount of cells.
-    points_with_cells : array
-        Array with points connected to cells.
-    points_without_cells : array
-        Array with points not connected to cells.
-    cells_per_point : array
-        Array which counts connected cells per point. Used for averging results.
 
     """
 
@@ -72,36 +76,20 @@ def __init__(self, points, cells, cell_type=None):
         self.cells = np.array(cells)
         self.cell_type = cell_type
 
-        self.update(self.cells)
-
-    def update(self, cells, cell_type=None):
-        "Update the cell and dimension attributes with a given cell array."
-        self.cells = cells
+        super().__init__(points=points, cells=cells, cell_type=cell_type)
 
-        if cell_type is not None:
-            self.cell_type = cell_type
+        self.__mesh__ = Mesh
 
-        # obtain dimensions
-        self.npoints, self.dim = self.points.shape
-        self.ndof = self.points.size
-        self.ncells = self.cells.shape[0]
-
-        # get number of cells per point
-        points_in_cell, self.cells_per_point = np.unique(cells, return_counts=True)
+    def __repr__(self):
+        header = "<felupe mesh object>"
+        points = f"  Number of points: {len(self.points)}"
+        cells_header = "  Number of cells:"
+        cells = [f"    {self.cell_type}: {self.ncells}"]
 
-        # check if there are points without cells
-        if self.npoints != len(self.cells_per_point):
-            self.point_has_cell = np.isin(np.arange(self.npoints), points_in_cell)
-            # update "cells_per_point" ... cells per point
-            cells_per_point = -np.ones(self.npoints, dtype=int)
-            cells_per_point[points_in_cell] = self.cells_per_point
-            self.cells_per_point = cells_per_point
+        return "\n".join([header, points, cells_header, *cells])
 
-            self.points_without_cells = np.arange(self.npoints)[~self.point_has_cell]
-            self.points_with_cells = np.arange(self.npoints)[self.point_has_cell]
-        else:
-            self.points_without_cells = np.array([], dtype=int)
-            self.points_with_cells = np.arange(self.npoints)
+    def __str__(self):
+        return self.__repr__()
 
     def disconnect(self, points_per_cell=None, calc_points=True):
         """Return a new instance of a Mesh with disconnected cells. Optionally, the
@@ -160,13 +148,88 @@ def copy(self):
 
         return deepcopy(self)
 
-    def __repr__(self):
-        header = "<felupe mesh object>"
-        points = f"  Number of points: {len(self.points)}"
-        cells_header = "  Number of cells:"
-        cells = [f"    {self.cell_type}: {self.ncells}"]
+    @wraps(expand)
+    def expand(self, n=11, z=1):
+        return as_mesh(expand(self, n=n, z=z))
+
+    @wraps(rotate)
+    def rotate(self, angle_deg, axis, center=None):
+        return as_mesh(rotate(self, angle_deg=angle_deg, axis=axis, center=center))
+
+    @wraps(revolve)
+    def revolve(self, n=11, phi=180, axis=0):
+        return as_mesh(revolve(self, n=n, phi=phi, axis=axis))
+
+    @wraps(sweep)
+    def sweep(self, decimals=None):
+        return as_mesh(sweep(self, decimals=decimals))
+
+    @wraps(mirror)
+    def mirror(self, normal=[1, 0, 0], centerpoint=[0, 0, 0], axis=None):
+        return as_mesh(mirror(self, normal=normal, centerpoint=centerpoint, axis=axis))
+
+    @wraps(triangulate)
+    def triangulate(self, mode=3):
+        return as_mesh(triangulate(self, mode=mode))
+
+    @wraps(runouts)
+    def add_runouts(
+        self,
+        values=[0.1, 0.1],
+        centerpoint=[0, 0, 0],
+        axis=0,
+        exponent=5,
+        mask=slice(None),
+    ):
+        return as_mesh(
+            runouts(
+                self,
+                values=values,
+                centerpoint=centerpoint,
+                axis=axis,
+                exponent=exponent,
+                mask=mask,
+            )
+        )
+
+    @wraps(convert)
+    def convert(
+        self,
+        order=0,
+        calc_points=False,
+        calc_midfaces=False,
+        calc_midvolumes=False,
+    ):
+        return as_mesh(
+            convert(
+                self,
+                order=order,
+                calc_points=calc_points,
+                calc_midfaces=calc_midfaces,
+                calc_midvolumes=calc_midvolumes,
+            )
+        )
 
-        return "\n".join([header, points, cells_header, *cells])
+    @wraps(collect_edges)
+    def collect_edges(self):
+        return collect_edges
 
-    def __str__(self):
-        return self.__repr__()
+    @wraps(collect_faces)
+    def collect_faces(self):
+        return collect_faces
+
+    @wraps(collect_volumes)
+    def collect_volumes(self):
+        return collect_volumes
+
+    @wraps(add_midpoints_edges)
+    def add_midpoints_edges(self):
+        return add_midpoints_edges
+
+    @wraps(add_midpoints_faces)
+    def add_midpoints_faces(self):
+        return add_midpoints_faces
+
+    @wraps(add_midpoints_volumes)
+    def add_midpoints_volumes(self):
+        return add_midpoints_volumes

src/felupe/mesh/_tools.py

@@ -29,7 +29,6 @@
 
 from ..math import rotation_matrix
 from ._helpers import mesh_or_data
-from ._mesh import Mesh
 
 
 @mesh_or_data
@@ -332,6 +331,8 @@ def mirror(
 def concatenate(meshes):
     "Join a sequence of meshes with identical cell types."
 
+    Mesh = meshes[0].__mesh__
+
     points = np.vstack([mesh.points for mesh in meshes])
     offsets = np.cumsum(np.insert([mesh.npoints for mesh in meshes][:-1], 0, 0))
     cells = np.vstack([offset + mesh.cells for offset, mesh in zip(offsets, meshes)])