GEOPY-2152: Bad referencing to transmitter id name

simpeg_drivers-assets/uijson/induced_polarization_2d_forward.ui.json

@@ -135,7 +135,7 @@
         "parent": "mesh",
         "label": "Value(s)",
         "property": "",
-        "value": 0.0
+        "value": 0.0001
     },
     "topography_object": {
         "main": true,

simpeg_drivers-assets/uijson/induced_polarization_2d_inversion.ui.json

@@ -154,7 +154,7 @@
         "parent": "mesh",
         "label": "Initial chargeability (V/V)",
         "property": "",
-        "value": 0.0
+        "value": 0.0001
     },
     "reference_model": {
         "association": "Cell",

simpeg_drivers-assets/uijson/induced_polarization_3d_forward.ui.json

@@ -68,7 +68,7 @@
         "property": "",
         "min": 0.0,
         "max": 10000.0,
-        "value": 0.0
+        "value": 0.0001
     },
     "topography_object": {
         "main": true,

simpeg_drivers-assets/uijson/induced_polarization_3d_inversion.ui.json

@@ -93,7 +93,7 @@
         "property": "",
         "min": 0.0,
         "max": 10000.0,
-        "value": 0.0
+        "value": 0.0001
     },
     "reference_model": {
         "association": [

simpeg_drivers-assets/uijson/induced_polarization_batch2d_forward.ui.json

@@ -117,7 +117,7 @@
         "parent": "mesh",
         "label": "Value(s)",
         "property": "",
-        "value": 0.001
+        "value": 0.0001
     },
     "topography_object": {
         "main": true,

simpeg_drivers-assets/uijson/induced_polarization_batch2d_inversion.ui.json

@@ -136,7 +136,7 @@
         "parent": "mesh",
         "label": "Initial chargeability (V/V)",
         "property": "",
-        "value": 0.001
+        "value": 0.0001
     },
     "reference_model": {
         "association": "Cell",

simpeg_drivers/components/factories/__init__.py

@@ -19,7 +19,7 @@
 from .entity_factory import EntityFactory
 from .misfit_factory import MisfitFactory
 from .simulation_factory import SimulationFactory
-from .survey_factory import SurveyFactory, receiver_group
+from .survey_factory import SurveyFactory
 
 # pylint: disable=unused-import
 # flake8: noqa

simpeg_drivers/components/factories/survey_factory.py

@@ -33,39 +33,6 @@
 from simpeg_drivers.components.factories.source_factory import SourcesFactory
 
 
-def receiver_group(txi, potential_electrodes):
-    """
-    Group receivers by common transmitter id.
-
-    :param: txi : transmitter index number.
-    :param: potential_electrodes : geoh5py object that holds potential electrodes
-        ab_map and ab_cell_id for a dc survey.
-
-    :return: ids : list of ids of potential electrodes used with transmitter txi.
-    """
-
-    index_map = potential_electrodes.ab_map()
-    index_map = {int(v): k for k, v in index_map.items() if v != "Unknown"}
-    ids = np.where(
-        potential_electrodes.ab_cell_id.values.astype(int) == index_map[txi]
-    )[0]
-
-    return ids
-
-
-def group_locations(obj, ids):
-    """
-    Return vertex locations for possible group of cells.
-
-    :param obj : geoh5py object containing cells, vertices structure.
-    :param ids : list of ids (or possibly single id) that indexes cells array.
-
-    :return locations : tuple of n locations arrays where n is length of second
-        dimension of cells array.
-    """
-    return (obj.vertices[obj.cells[ids, i]] for i in range(obj.cells.shape[1]))
-
-
 class SurveyFactory(SimPEGFactory):
     """Build SimPEG sources objects based on factory type."""
 
@@ -289,7 +256,9 @@ def _dcip_arguments(self, data=None, local_index=None):
         sources = []
         self.local_index = []
         for source_id in source_ids[np.argsort(order)]:  # Cycle in original order
-            receiver_indices = receiver_group(source_id, receiver_entity)
+            receiver_indices = np.where(receiver_entity.ab_cell_id.values == source_id)[
+                0
+            ]
 
             if local_index is not None:
                 receiver_indices = list(set(receiver_indices).intersection(local_index))

simpeg_drivers/components/topography.py

@@ -164,13 +164,16 @@ def expand_actives(
             neighbours = get_neighbouring_cells(mesh.mesh, containing_cells)
             neighbours_xy = np.r_[neighbours[0] + neighbours[1]]
 
+            neighbours_xy = neighbours_xy[neighbours_xy != -1]
             # Make sure the new actives are connected to the old actives
             new_actives = ~active_cells[neighbours_xy]
             if np.any(new_actives):
                 neighbours = get_neighbouring_cells(
                     mesh.mesh, neighbours_xy[new_actives]
                 )
-                active_cells[np.r_[neighbours[2][0]]] = True  # z-axis neighbours
+                neighbours_z = np.r_[neighbours[2][0]]
+                neighbours_z = neighbours_z[neighbours_z != -1]
+                active_cells[neighbours_z] = True  # z-axis neighbours
 
             active_cells[neighbours_xy] = True  # xy-axis neighbours
 

simpeg_drivers/options.py

@@ -27,7 +27,7 @@
     ReferencedData,
 )
 from geoh5py.groups import PropertyGroup, SimPEGGroup, UIJsonGroup
-from geoh5py.objects import DrapeModel, Octree, Points
+from geoh5py.objects import DrapeModel, Grid2D, Octree, Points
 from geoh5py.shared.utils import fetch_active_workspace
 from geoh5py.ui_json import InputFile
 from pydantic import BaseModel, ConfigDict, field_validator, model_validator
@@ -54,7 +54,7 @@ class ActiveCellsOptions(BaseModel):
     model_config = ConfigDict(
         arbitrary_types_allowed=True,
     )
-    topography_object: Points | None = None
+    topography_object: Points | Grid2D | None = None
     topography: FloatData | float | None = None
     active_model: BooleanData | IntegerData | None = None
 

tests/topography_test.py

@@ -14,14 +14,14 @@
 
 import numpy as np
 
-from simpeg_drivers.components import InversionTopography
+from simpeg_drivers.components import InversionData, InversionMesh, InversionTopography
 from simpeg_drivers.options import ActiveCellsOptions
 from simpeg_drivers.potential_fields import MVIInversionOptions
 from simpeg_drivers.utils.testing import Geoh5Tester, setup_inversion_workspace
 
 
 def test_get_locations(tmp_path: Path):
-    geoh5, entity, model, survey, topography = setup_inversion_workspace(
+    geoh5, mesh, model, survey, topography = setup_inversion_workspace(
         tmp_path,
         background=0.0,
         anomaly=0.05,
@@ -31,7 +31,6 @@ def test_get_locations(tmp_path: Path):
         inversion_type="magnetic_vector",
     )
     with geoh5.open():
-        mesh = model.parent
         tmi_channel, gyz_channel = survey.add_data(
             {
                 "tmi": {"values": np.random.rand(survey.n_vertices)},
@@ -51,6 +50,7 @@ def test_get_locations(tmp_path: Path):
         ),
         starting_model=1.0,
     )
+
     geoh5 = params.geoh5
     with geoh5.open():
         topo = InversionTopography(geoh5, params)
@@ -60,6 +60,25 @@ def test_get_locations(tmp_path: Path):
             params.active_cells.topography.values,
         )
 
+        # Check that boundary cells are handled properly
+        # Shift one of the survey vertices to the corner
+        survey.vertices[0, :] = mesh.centroids[0, :]
+        geoh5.update_attribute(survey, "vertices")
+        inversion_mesh = InversionMesh(geoh5, params)
+        inversion_data = InversionData(geoh5, params)
+        params.inversion_type = "magnetotellurics"
+        active_cells = topo.active_cells(inversion_mesh, inversion_data)
+
+        mesh.add_data(
+            {
+                "active_cells": {
+                    "values": active_cells,
+                }
+            }
+        )
+        assert not active_cells[-1]
+
+        # Test flat topo
         params.active_cells.topography = 199.0
         locs = topo.get_locations(params.active_cells.topography_object)
         np.testing.assert_allclose(locs[:, 2], np.ones_like(locs[:, 2]) * 199.0)