Fix bug with mesh indexing for start_index=1

changelog/7253.bugfix.rst

@@ -0,0 +1,2 @@
+:user:`stephenworsley` fixed a bug which caused indexing to fail when
+``start_index`` was 1. (:issue:`7246`)

lib/iris/mesh/components.py

@@ -3132,6 +3132,7 @@ def indexed(
                     #  used by MeshCoord, which also maintains laziness.
                     indices = connectivity.lazy_indices()
                 indices_indexed = connectivity.indices_by_location(indices)[indexing]
+                indices_indexed -= connectivity.start_index
 
                 # Map node indices in "values" to their new zero-based positions
                 #  via the inverse-lookup table. This creates a contiguous
@@ -3524,6 +3525,7 @@ def _calculate_node_bool_index(self):
                 conn_indices = connectivity.indices_by_location(
                     connectivity.core_indices()
                 )[self.indices]
+                conn_indices -= connectivity.start_index
                 al = da if _lazy.is_lazy_data(conn_indices) else np
                 # Flatten and drop masked padding (ragged connectivities) by scattering
                 #  membership into a fixed-shape boolean mask.

lib/iris/tests/integration/mesh/test_indexing_meshes.py

@@ -3,6 +3,7 @@
 # This file is part of Iris and is released under the BSD license.
 # See LICENSE in the root of the repository for full licensing details.
 
+import numpy as np
 import pytest
 
 from iris.coords import AuxCoord, Coord
@@ -47,6 +48,17 @@ def cube_mesh_face():
     return (sample_mesh_cube(location=location, mesh=mesh), location)
 
 
+@pytest.fixture
+def cube_mesh_1_indexed(cube_mesh_from_file):
+    cube = cube_mesh_from_file[0]
+    mesh = cube.mesh
+    for con in mesh.all_connectivities:
+        if con is not None:
+            con.indices[:] += 1
+            con._metadata_manager.start_index = 1
+    return (cube, "face")
+
+
 def change_and_assert_no_change_in_right(left: Coord, right: Coord, value: int):
     left.points[0] = value
     assert right.points[0] != value
@@ -187,3 +199,34 @@ def change_original_mesh_reflected_in_index_set(
     change_original_mesh_reflected_in_index_set(
         cube, indexed_cube, "longitude", location, value
     )
+
+
+@pytest.mark.parametrize(
+    "fixture",
+    ["cube_mesh_from_file", "cube_mesh_edge", "cube_mesh_face", "cube_mesh_1_indexed"],
+)
+def test_indexing_mode_equivalency(fixture, request):
+    cube: Cube
+    location: str
+    (cube, location) = request.getfixturevalue(fixture)
+
+    with mesh_coord_indexing.SETTING.context(mesh_coord_indexing.Options.AUX_COORD):
+        indexed_cube_aux = cube[0, 1:-1]
+    with mesh_coord_indexing.SETTING.context(mesh_coord_indexing.Options.NEW_MESH):
+        indexed_cube_mesh = cube[0, 1:-1]
+    with mesh_coord_indexing.SETTING.context(
+        mesh_coord_indexing.Options.MESH_INDEX_SET
+    ):
+        indexed_cube_mis = cube[0, 1:-1]
+
+    aux_lon = indexed_cube_aux.coord("longitude")
+    aux_lat = indexed_cube_aux.coord("latitude")
+    mesh_lon = indexed_cube_mesh.coord("longitude")
+    mesh_lat = indexed_cube_mesh.coord("latitude")
+    mis_lon = indexed_cube_mis.coord("longitude")
+    mis_lat = indexed_cube_mis.coord("latitude")
+
+    assert np.array_equal(aux_lon.bounds, mesh_lon.bounds)
+    assert np.array_equal(aux_lat.bounds, mesh_lat.bounds)
+    assert np.array_equal(aux_lon.bounds, mis_lon.bounds)
+    assert np.array_equal(aux_lat.bounds, mis_lat.bounds)

lib/iris/tests/unit/mesh/components/test_MeshIndexSet.py

@@ -513,12 +513,27 @@ def varied_mesh(self, lazy_values):
         )
         return mesh
 
-    def test_varied_faces(self, varied_mesh):
+    @pytest.fixture
+    def varied_mesh_1_indexed(self, varied_mesh):
         mesh = varied_mesh
+        for con in mesh.all_connectivities:
+            if con is not None:
+                con.indices[:] += 1
+                con._metadata_manager.start_index = 1
+        return mesh
+
+    @pytest.mark.parametrize(
+        "fixture",
+        ["varied_mesh", "varied_mesh_1_indexed"],
+    )
+    def test_varied_faces(self, fixture, request):
+        mesh: MeshXY = request.getfixturevalue(fixture)
         index_set = _MeshIndexSet(indices=[0, 1, 3], mesh=mesh, location="face")
         _shared_utils.assert_array_equal(index_set.indices, np.array([0, 1, 3]))
+        connectivity = index_set.connectivity(cf_role="face_node_connectivity")
+        normalised_indices = connectivity.indices - connectivity.start_index
         _shared_utils.assert_array_equal(
-            index_set.connectivity(cf_role="face_node_connectivity").indices,
+            normalised_indices,
             np.ma.masked_array(
                 data=[[7, 8, 10, 9, -1], [3, 7, 6, -1, -1], [0, 1, 2, 5, 4]],
                 mask=[[0, 0, 0, 0, 1], [0, 0, 0, 1, 1], [0, 0, 0, 0, 0]],
@@ -532,12 +547,18 @@ def test_varied_faces(self, varied_mesh):
             np.array([-2, -3, -4, -1, -3, -4, -1, -2, -3, -2, -3]),
         )
 
-    def test_varied_edges(self, varied_mesh):
-        mesh = varied_mesh
+    @pytest.mark.parametrize(
+        "fixture",
+        ["varied_mesh", "varied_mesh_1_indexed"],
+    )
+    def test_varied_edges(self, fixture, request):
+        mesh: MeshXY = request.getfixturevalue(fixture)
         index_set = _MeshIndexSet(indices=[0, 1, 4], mesh=mesh, location="edge")
         _shared_utils.assert_array_equal(index_set.indices, np.array([0, 1, 4]))
+        connectivity = index_set.connectivity(cf_role="edge_node_connectivity")
+        normalised_indices = connectivity.indices - connectivity.start_index
         _shared_utils.assert_array_equal(
-            index_set.connectivity(cf_role="edge_node_connectivity").indices,
+            normalised_indices,
             # Note the shared node.
             np.array([[0, 1], [1, 2], [3, 4]]),
         )