fix(tidy3d): FXC-4824-fix-corrupted-data-in-vtk-arrays

Author: marcorudolphflex

tidy3d/components/data/unstructured/base.py

@@ -729,7 +729,7 @@ def _get_values_from_vtk(
                     f" of grid points ({num_points})."
                 )
 
-            values_numpy = vtk["vtk_to_numpy"](array_vtk)
+            values_numpy = np.array(vtk["vtk_to_numpy"](array_vtk), copy=True)
             values_name = array_vtk.GetName()
 
             # vtk doesn't support complex numbers
@@ -1260,12 +1260,17 @@ def _interp_vtk(
         array_id = 0 if self.values.name is None else self.values.name
 
         # TODO: generalize this
-        values_numpy = vtk["vtk_to_numpy"](interpolated.GetPointData().GetAbstractArray(array_id))
+        values_numpy = np.array(
+            vtk["vtk_to_numpy"](interpolated.GetPointData().GetAbstractArray(array_id)), copy=True
+        )
 
         # fill points without interpolated values
         if fill_value != 0:
-            mask = vtk["vtk_to_numpy"](
-                interpolated.GetPointData().GetAbstractArray("vtkValidPointMask")
+            mask = np.array(
+                vtk["vtk_to_numpy"](
+                    interpolated.GetPointData().GetAbstractArray("vtkValidPointMask")
+                ),
+                copy=True,
             )
             values_numpy[mask != 1] = fill_value
 

tidy3d/components/data/unstructured/tetrahedral.py

@@ -105,18 +105,24 @@ def _from_vtk_obj(
         """Initialize from a vtkUnstructuredGrid instance."""
 
         # read point, cells, and values info from a vtk instance
-        cells_numpy = vtk["vtk_to_numpy"](vtk_obj.GetCells().GetConnectivityArray())
-        points_numpy = vtk["vtk_to_numpy"](vtk_obj.GetPoints().GetData())
+        cells_numpy = np.array(
+            vtk["vtk_to_numpy"](vtk_obj.GetCells().GetConnectivityArray()),
+            copy=True,
+        )
+        points_numpy = np.array(vtk["vtk_to_numpy"](vtk_obj.GetPoints().GetData()), copy=True)
         values = cls._get_values_from_vtk(
             vtk_obj, len(points_numpy), field, values_type, expect_complex
         )
 
         # verify cell_types
-        cells_types = vtk["vtk_to_numpy"](vtk_obj.GetCellTypesArray())
+        cells_types = np.array(vtk["vtk_to_numpy"](vtk_obj.GetCellTypesArray()), copy=True)
         invalid_cells = cells_types != cls._vtk_cell_type()
         if any(invalid_cells):
             if ignore_invalid_cells:
-                cell_offsets = vtk["vtk_to_numpy"](vtk_obj.GetCells().GetOffsetsArray())
+                cell_offsets = np.array(
+                    vtk["vtk_to_numpy"](vtk_obj.GetCells().GetOffsetsArray()),
+                    copy=True,
+                )
                 valid_cell_offsets = cell_offsets[:-1][invalid_cells == 0]
                 cells_numpy = cells_numpy[
                     np.ravel(

tidy3d/components/data/unstructured/triangular.py

@@ -149,10 +149,13 @@ def _from_vtk_obj(
         elif isinstance(vtk_obj, vtk["mod"].vtkUnstructuredGrid):
             cells_vtk = vtk_obj.GetCells()
 
-        cells_numpy = vtk["vtk_to_numpy"](cells_vtk.GetConnectivityArray())
+        cells_numpy = np.array(
+            vtk["vtk_to_numpy"](cells_vtk.GetConnectivityArray()),
+            copy=True,
+        )
 
         # verify cell_types
-        cell_offsets = vtk["vtk_to_numpy"](cells_vtk.GetOffsetsArray())
+        cell_offsets = np.array(vtk["vtk_to_numpy"](cells_vtk.GetOffsetsArray()), copy=True)
         invalid_cells = np.diff(cell_offsets) != cls._cell_num_vertices()
         if np.any(invalid_cells):
             if ignore_invalid_cells:
@@ -166,7 +169,7 @@ def _from_vtk_obj(
                     "'TriangularGridDataset'."
                 )
 
-        points_numpy = vtk["vtk_to_numpy"](vtk_obj.GetPoints().GetData())
+        points_numpy = np.array(vtk["vtk_to_numpy"](vtk_obj.GetPoints().GetData()), copy=True)
 
         # data values are read directly into Tidy3D array
         values = cls._get_values_from_vtk(
@@ -250,7 +253,7 @@ def plane_slice(self, axis: Axis, pos: float) -> XrDataArray:
 
         # perform slicing in vtk and get unprocessed points and values
         slice_vtk = self._plane_slice_raw(axis=axis, pos=pos)
-        points_numpy = vtk["vtk_to_numpy"](slice_vtk.GetPoints().GetData())
+        points_numpy = np.array(vtk["vtk_to_numpy"](slice_vtk.GetPoints().GetData()), copy=True)
         values = self._get_values_from_vtk(
             slice_vtk,
             len(points_numpy),