GEOPY-2590: Add validator for negative on NDV values in uncertainties

simpeg_drivers/options.py

@@ -18,6 +18,7 @@
 
 import numpy as np
 from geoapps_utils.base import Options
+from geoapps_utils.utils.importing import GeoAppsError
 from geoh5py.data import (
     BooleanData,
     DataAssociationEnum,
@@ -458,7 +459,7 @@ def property_group_data(self, property_group: PropertyGroup):
             k for k in self.data_object.property_groups if k.uid == property_group.uid
         )
         data = {
-            freq: self.geoh5.get_entity(p)[0].values
+            freq: self.data_object.get_entity(p)[0].values
             for freq, p in zip(frequencies, group.properties, strict=False)
         }
         return data
@@ -615,20 +616,35 @@ def data(self) -> dict[str, dict[float, np.ndarray | None]]:
 
     @property
     def uncertainties(self) -> dict[str, dict[float, np.ndarray | None]]:
-        """Return dictionary of unceratinty components and associated values."""
+        """Return dictionary of uncertainty components and associated values."""
         out = {}
+        flags = []
         for k in self.active_components:
             out[k] = self.component_uncertainty(k)
+
+            for data in out[k].values():
+                if np.any(np.isnan(data)) or np.any(data < 0):
+                    flags.append(f"{k} component")
+                    break
+
+        if flags:
+            summary = (
+                "Issues encountered with uncertainties having NDV or negative values:\n\n - "
+                + "\n - ".join(flags)
+            )
+            summary += "\n\nPlease review the input values."
+            raise GeoAppsError(summary)
+
         return out
 
-    def component_data(self, component: str) -> np.ndarray | None:
+    def component_data(self, component: str) -> dict:
         """Return data values associated with the component."""
         data = getattr(self, "_".join([component, "channel"]), None)
         if isinstance(data, NumericData):
             data = data.values
         return {None: data}
 
-    def component_uncertainty(self, component: str) -> np.ndarray | None:
+    def component_uncertainty(self, component: str) -> dict:
         """
         Return uncertainty values associated with the component.
 

tests/run_tests/driver_grav_test.py

@@ -206,6 +206,32 @@ def test_array_too_large_run(
             driver.run()
 
 
+def test_bad_uncertainties(
+    tmp_path: Path,
+):
+    workpath = tmp_path / f"{__name__}.ui.geoh5"
+
+    with Workspace(workpath) as geoh5:
+        components = SyntheticsComponents(geoh5)
+        gz = components.survey.add_data(
+            {"data": {"values": np.random.randn(components.survey.n_vertices)}}
+        )
+
+        # Run the inverse
+        params = GravityInversionOptions.build(
+            geoh5=geoh5,
+            mesh=components.mesh,
+            topography_object=components.topography,
+            data_object=gz.parent,
+            gz_channel=gz,
+            gz_uncertainty=-1e-4,
+            starting_model=1e-4,
+        )
+
+        with raises(GeoAppsError, match="Issues encountered with uncertainties"):
+            _ = params.uncertainties
+
+
 if __name__ == "__main__":
     # Full run
     test_gravity_fwr_run(

tests/run_tests/driver_mt_test.py

@@ -15,7 +15,9 @@
 from pathlib import Path
 
 import numpy as np
+from geoapps_utils.utils.importing import GeoAppsError
 from geoh5py.workspace import Workspace
+from pytest import raises
 
 from simpeg_drivers.natural_sources.magnetotellurics import (
     MTForwardDriver,
@@ -73,7 +75,7 @@ def setup_data(workspace, survey):
                     }
                 }
             )
-            uncertainties[f"{cname} uncertainties"].append(uncert.copy(parent=survey))
+            uncertainties[f"{cname} uncertainties"].append(uncert)
 
     data_groups = survey.add_components_data(data)
     uncert_groups = survey.add_components_data(uncertainties)
@@ -141,6 +143,47 @@ def test_magnetotellurics_fwr_run(
         assert geoh5.get_entity("Iteration_0_zyy_real_[0]")[0] is not None
 
 
+def test_bad_uncertainties(
+    tmp_path: Path,
+):
+    workpath = (
+        tmp_path.parent / "test_magnetotellurics_fwr_run0" / "inversion_test.ui.geoh5"
+    )
+
+    with Workspace(workpath) as geoh5:
+        with Workspace.create(tmp_path / f"{__name__}.geoh5") as ws:
+            components = SyntheticsComponents(geoh5)
+            survey = components.survey.copy(
+                parent=ws, copy_children=False, name="bad_uncertainties"
+            )
+            mesh = components.mesh
+            topography = components.topography
+            data_kwargs = setup_data(geoh5, survey)
+
+            for elem in ["uncertainty_zxx_imag_[0]", "uncertainty_zyx_real_[0]"]:
+                data = survey.get_entity(elem)[0]
+                vals = data.values
+                vals[0] = np.nan
+                data.values = vals
+
+            # Run the inverse
+            params = MTInversionOptions.build(
+                geoh5=geoh5,
+                mesh=mesh,
+                topography_object=topography,
+                data_object=survey,
+                starting_model=100.0,
+                background_conductivity=100.0,
+                **data_kwargs,
+            )
+
+            with raises(GeoAppsError) as error:
+                _ = params.uncertainties
+
+    assert "zxx_imag" in str(error.value)
+    assert "zyx_real" in str(error.value)
+
+
 def test_magnetotellurics_run(tmp_path: Path, max_iterations=1, pytest=True):
     # pass
     workpath = tmp_path / "inversion_test.ui.geoh5"