Merge pull request #995 from nschloe/gh-993

fix for remove_orphaned_nodes()

meshio/_mesh.py

@@ -124,6 +124,10 @@ def remove_orphaned_nodes(self):
         """Remove nodes which don't belong to any cell."""
         all_cells_flat = numpy.concatenate([c.data.flat for c in self.cells])
         orphaned_nodes = numpy.setdiff1d(numpy.arange(len(self.points)), all_cells_flat)
+
+        if len(orphaned_nodes) == 0:
+            return
+
         self.points = numpy.delete(self.points, orphaned_nodes, axis=0)
         # also adapt the point data
         self.point_data = {
@@ -133,19 +137,21 @@ def remove_orphaned_nodes(self):
 
         # reset GLOBAL_ID
         if "GLOBAL_ID" in self.point_data:
+            n = len(self.point_data["GLOBAL_ID"])
+            assert numpy.all(self.point_data["GLOBAL_ID"] == numpy.arange(1, n + 1))
             self.point_data["GLOBAL_ID"] = numpy.arange(1, len(self.points) + 1)
 
         # We now need to adapt the cells too.
         diff = numpy.zeros(len(all_cells_flat), dtype=all_cells_flat.dtype)
         for orphan in orphaned_nodes:
             diff[numpy.argwhere(all_cells_flat > orphan)] += 1
         all_cells_flat -= diff
-        k = 0
+        i = 0
         for k, c in enumerate(self.cells):
             s = c.data.shape
             n = numpy.prod(s)
-            self.cells[k] = CellBlock(c.type, all_cells_flat[k : k + n].reshape(s))
-            k += n
+            self.cells[k] = CellBlock(c.type, all_cells_flat[i : i + n].reshape(s))
+            i += n
 
     def prune_z_0(self, tol: float = 1.0e-13):
         """Remove third (z) component of points if it is 0 everywhere (up to a

setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
 name = meshio
-version = 4.3.6
+version = 4.3.7
 author = Nico Schlömer et al.
 author_email = [email protected]
 description = I/O for many mesh formats

test/test_mesh.py

@@ -23,13 +23,13 @@ def test_print_prune():
 def test_remove_orphaned():
     points = numpy.array(
         [
+            [3.14, 2.71],  # orphaned
             [0.0, 0.0],
             [1.0, 0.0],
             [0.0, 1.0],
-            [3.14, 2.71],  # orphaned
         ]
     )
-    cells = numpy.array([[0, 1, 2]])
+    cells = numpy.array([[1, 2, 3]])
     a = {"a": numpy.array([0.1, 0.2, 0.3, 0.4])}
     mesh = meshio.Mesh(points, {"triangle": cells}, point_data=a)
     mesh.remove_orphaned_nodes()
@@ -39,6 +39,7 @@ def test_remove_orphaned():
     # make sure the dict `a` wasn't changed,
     # <https://github.com/nschloe/meshio/pull/994>
     assert len(a["a"]) == 4
+    assert numpy.all(mesh.cells[0].data == [0, 1, 2])
 
 
 def test_cells_dict():