Merge pull request #1218 from nschloe/copy

mesh.copy(), mesh.deduplicate_points()

setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
 name = meshio
-version = 5.0.2
+version = 5.0.3
 author = Nico Schlömer et al.
 author_email = [email protected]
 description = I/O for many mesh formats
@@ -39,6 +39,7 @@ package_dir =
 packages = find:
 install_requires =
     importlib_metadata;python_version<"3.8"
+    npx >= 0.0.22
     numpy
 python_requires = >=3.7
 

src/meshio/_mesh.py

@@ -1,8 +1,10 @@
 from __future__ import annotations
 
 import collections
+import copy
 import warnings
 
+import npx
 import numpy as np
 
 from ._common import _topological_dimension, num_nodes_per_cell
@@ -132,6 +134,9 @@ def __repr__(self):
 
         return "\n".join(lines)
 
+    def copy(self):
+        return copy.deepcopy(self)
+
     def prune(self):
         # nschloe, 2020-11:
         warnings.warn(
@@ -407,3 +412,25 @@ def int_data_to_sets(self):
         # remove the cell data
         for key in keys:
             del self.point_data[key]
+
+    def deduplicate_points(self, tol: float) -> int:
+        num_points_before = len(self.points)
+
+        unique_points, idx, inv = npx.unique(
+            self.points, tol=tol, axis=0, return_index=True, return_inverse=True
+        )
+        self.points = unique_points
+        num_removed_points = num_points_before - len(self.points)
+
+        # re-index cell blocks
+        self.cells = [CellBlock(cb.type, inv[cb.data]) for cb in self.cells]
+
+        # reset point data
+        for key, values in self.point_data.items():
+            self.point_data[key] = values[idx]
+
+        # reset point sets
+        for key, values in self.point_sets.items():
+            self.point_sets[key] = inv[values]
+
+        return num_removed_points

tests/test_mesh.py

@@ -136,6 +136,41 @@ def test_gh_1165():
     assert_equal(mesh.cell_sets, {"test": [[], [1]], "sets": [[0, 1], [0, 2, 3]]})
 
 
+def test_copy():
+    mesh = helpers.tri_mesh
+    mesh2 = mesh.copy()
+
+    assert np.all(mesh.points == mesh2.points)
+    assert not np.may_share_memory(mesh.points, mesh2.points)
+
+
+def test_deduplicate_points():
+    points = np.array(
+        [
+            [0.0, 0.0],
+            [1.0, 0.0],
+            [1.0, 1.0],
+            [1.0, 0.0],
+            [1.0, 1.0],
+            [2.0, 0.0],
+        ]
+    )
+    point_data = {"a": [0.1, 0.2, 0.3, 0.4, 0.5, 0.6]}
+    point_sets = {"b": [0, 4, 5]}
+    cells = [[0, 1, 2], [3, 4, 5]]
+    mesh = meshio.Mesh(
+        points, {"triangle": cells}, point_data=point_data, point_sets=point_sets
+    )
+
+    num_removed_points = mesh.deduplicate_points(1.0e-10)
+    assert num_removed_points == 2
+    assert np.all(mesh.points == [[0.0, 0.0], [1.0, 0.0], [1.0, 1.0], [2.0, 0.0]])
+    assert np.all(mesh.cells[0].data == [[0, 1, 2], [1, 2, 3]])
+
+    assert np.all(mesh.point_data["a"] == [0.1, 0.2, 0.3, 0.6])
+    assert np.all(mesh.point_sets["b"] == [0, 2, 3])
+
+
 if __name__ == "__main__":
     # test_sets_to_int_data()
     test_int_data_to_sets()