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Merge pull request #244 from MiraGeoscience/GEOPY-1302
GEOPY-1302: Organize geoapps.utils.testing.setup_inversion_workspace
2 parents 170f3cc + 751912a commit 86209cb

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Lines changed: 2741 additions & 1959 deletions

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‎.pre-commit-config.yaml‎

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- id: mixed-line-ending
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exclude: ^\.idea/.*\.xml$
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- id: name-tests-test
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exclude: testing_utils.py
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exclude: targets.py
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- id: pretty-format-json
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args:
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- --autofix

‎simpeg_drivers/utils/synthetics/__init__.py‎

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# '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
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# Copyright (c) 2025 Mira Geoscience Ltd. '
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# '
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# This file is part of simpeg-drivers package. '
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# '
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# simpeg-drivers is distributed under the terms and conditions of the MIT License '
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# (see LICENSE file at the root of this source code package). '
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# '
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# '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''

‎simpeg_drivers/utils/synthetics/driver.py‎

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# '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
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# Copyright (c) 2025 Mira Geoscience Ltd. '
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# '
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# This file is part of simpeg-drivers package. '
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# '
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# simpeg-drivers is distributed under the terms and conditions of the MIT License '
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# (see LICENSE file at the root of this source code package). '
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# '
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# '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
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import numpy as np
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from geoh5py import Workspace
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from geoh5py.data import FloatData
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from geoh5py.objects import DrapeModel, ObjectBase, Octree, Surface
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from simpeg_drivers.utils.synthetics.meshes.factory import get_mesh
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from simpeg_drivers.utils.synthetics.models import get_model
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from simpeg_drivers.utils.synthetics.options import SyntheticsComponentsOptions
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from simpeg_drivers.utils.synthetics.surveys.factory import get_survey
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from simpeg_drivers.utils.synthetics.topography import (
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get_active,
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get_topography_surface,
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)
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class SyntheticsComponents:
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"""Creates a workspace populated with objects for simulation and subsequent inversion."""
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def __init__(
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self,
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geoh5: Workspace,
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options: SyntheticsComponentsOptions | None = None,
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):
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if options is None:
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options = SyntheticsComponentsOptions()
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self.geoh5 = geoh5
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self.options = options
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self._topography: Surface | None = None
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self._survey: ObjectBase | None = None
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self._mesh: Octree | DrapeModel | None = None
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self._active: FloatData | None = None
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self._model: FloatData | None = None
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@property
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def topography(self):
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entity = self.geoh5.get_entity("topography")[0]
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assert isinstance(entity, Surface | type(None))
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if entity is None:
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assert self.options is not None
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entity = get_topography_surface(
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geoh5=self.geoh5,
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options=self.options.survey,
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)
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self._topography = entity
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return self._topography
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@property
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def survey(self):
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entity = self.geoh5.get_entity(self.options.survey.name)[0]
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assert isinstance(entity, ObjectBase | type(None))
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if entity is None:
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assert self.options is not None
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entity = get_survey(
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geoh5=self.geoh5,
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method=self.options.method,
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options=self.options.survey,
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)
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self._survey = entity
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return self._survey
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@property
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def mesh(self):
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entity = self.geoh5.get_entity(self.options.mesh.name)[0]
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assert isinstance(entity, Octree | DrapeModel | type(None))
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if entity is None:
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assert self.options is not None
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entity = get_mesh(
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self.options.method,
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survey=self.survey,
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topography=self.topography,
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options=self.options.mesh,
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)
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self._mesh = entity
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return self._mesh
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@property
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def active(self):
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entity = self.geoh5.get_entity(self.options.active.name)[0]
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assert isinstance(entity, FloatData | type(None))
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if entity is None:
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entity = get_active(self.mesh, self.topography)
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self._active = entity
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return self._active
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@property
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def model(self):
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entity = self.geoh5.get_entity(self.options.model.name)[0]
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assert isinstance(entity, FloatData | type(None))
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if entity is None:
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assert self.options is not None
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entity = get_model(
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method=self.options.method,
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mesh=self.mesh,
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active=self.active.values,
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options=self.options.model,
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)
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self._model = entity
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return self._model

‎simpeg_drivers/utils/synthetics/meshes/__init__.py‎

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# '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
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# Copyright (c) 2025 Mira Geoscience Ltd. '
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# '
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# This file is part of simpeg-drivers package. '
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# '
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# simpeg-drivers is distributed under the terms and conditions of the MIT License '
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# (see LICENSE file at the root of this source code package). '
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# '
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# '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''

‎simpeg_drivers/utils/synthetics/meshes/factory.py‎

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# '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
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# Copyright (c) 2025 Mira Geoscience Ltd. '
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# '
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# This file is part of simpeg-drivers package. '
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# '
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# simpeg-drivers is distributed under the terms and conditions of the MIT License '
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# (see LICENSE file at the root of this source code package). '
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# '
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# '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
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from discretize import TensorMesh, TreeMesh
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from geoh5py.objects import CellObject, DrapeModel, Octree, Points, Surface
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from simpeg_drivers.utils.synthetics.options import MeshOptions
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from .octrees import get_octree_mesh
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from .tensors import get_tensor_mesh
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def get_mesh(
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method: str,
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survey: Points,
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topography: Surface,
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options: MeshOptions,
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) -> DrapeModel | Octree:
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"""Factory for mesh creation with behaviour modified by the provided method."""
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if "2d" in method:
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assert isinstance(survey, CellObject)
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return get_tensor_mesh(
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survey=survey,
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cell_size=options.cell_size,
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padding_distance=options.padding_distance,
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name=options.name,
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)
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return get_octree_mesh(
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survey=survey,
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topography=topography,
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cell_size=options.cell_size,
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refinement=options.refinement,
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padding_distance=options.padding_distance,
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refine_on_receivers=method in ["fdem", "airborne tdem"],
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name=options.name,
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)

‎simpeg_drivers/utils/synthetics/meshes/octrees.py‎

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# '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
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# Copyright (c) 2025 Mira Geoscience Ltd. '
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# '
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# This file is part of simpeg-drivers package. '
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# '
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# simpeg-drivers is distributed under the terms and conditions of the MIT License '
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# (see LICENSE file at the root of this source code package). '
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# '
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# '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
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import numpy as np
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from discretize import TreeMesh
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from discretize.utils import mesh_builder_xyz
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from geoh5py.objects import Octree, Points, Surface
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from octree_creation_app.driver import OctreeDriver
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from octree_creation_app.utils import treemesh_2_octree
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def get_base_octree(
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survey: Points,
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topography: Surface,
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cell_size: tuple[float, float, float],
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refinement: tuple,
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padding: float,
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) -> TreeMesh:
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"""
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Generate a survey centered TreeMesh object with topography refinement.
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:param survey: Survey object with vertices that define the core of the
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tensor mesh.
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:param topography: Surface used to refine the topography.
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:param cell_size: Tuple defining the cell size in all directions.
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:param refinement: Tuple containing the number of cells to refine at each
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level around the topography.
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:param padding: Distance to pad the mesh in all directions.
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:return mesh: The discretize TreeMesh object for computations.
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"""
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padding_distance = np.ones((3, 2)) * padding
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mesh = mesh_builder_xyz(
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survey.vertices - np.r_[cell_size] / 2.0,
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cell_size,
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depth_core=100.0,
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padding_distance=padding_distance,
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mesh_type="TREE",
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tree_diagonal_balance=False,
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)
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mesh = OctreeDriver.refine_tree_from_surface(
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mesh, topography, levels=refinement, finalize=False
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)
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return mesh
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def get_octree_mesh(
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survey: Points,
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topography: Surface,
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cell_size: tuple[float, float, float],
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refinement: tuple,
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padding_distance: float,
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refine_on_receivers: bool,
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name: str = "mesh",
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) -> Octree:
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"""Generate a survey centered mesh with topography and survey refinement.
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:param survey: Survey object with vertices that define the core of the
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tensor mesh and the source refinement for EM methods.
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:param topography: Surface used to refine the topography.
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:param cell_size: Tuple defining the cell size in all directions.
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:param refinement: Tuple containing the number of cells to refine at each
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level around the topography.
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:param padding: Distance to pad the mesh in all directions.
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:param refine_on_receivers: Refine on the survey locations or not.
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:return entity: The geoh5py Octree object to store the results of
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computation in the shared cells of the computational mesh.
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:return mesh: The discretize TreeMesh object for computations.
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"""
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mesh = get_base_octree(survey, topography, cell_size, refinement, padding_distance)
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if refine_on_receivers:
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mesh = OctreeDriver.refine_tree_from_points(
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mesh, survey.vertices, levels=[2], finalize=False
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)
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mesh.finalize()
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entity = treemesh_2_octree(survey.workspace, mesh, name=name)
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return entity

‎simpeg_drivers/utils/synthetics/meshes/tensors.py‎

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# '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
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# Copyright (c) 2025 Mira Geoscience Ltd. '
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# '
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# This file is part of simpeg-drivers package. '
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# '
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# simpeg-drivers is distributed under the terms and conditions of the MIT License '
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# (see LICENSE file at the root of this source code package). '
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# '
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# '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
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import numpy as np
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from geoh5py.data import IntegerData
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from geoh5py.objects import CellObject, DrapeModel
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from simpeg_drivers.utils.utils import get_drape_model
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def get_tensor_mesh(
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survey: CellObject,
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cell_size: tuple[float, float, float],
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padding_distance: float,
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line_id: int = 101,
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name: str = "mesh",
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) -> DrapeModel:
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"""
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Generate a tensor mesh and the colocated DrapeModel.
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:param survey: Survey object with vertices that define the core of the
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tensor mesh.
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:param cell_size: Tuple defining the cell size in all directions.
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:param padding_distance: Distance to pad the mesh in all directions.
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:param line_id: Chooses line from the survey to define the drape model.
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:return entity: The DrapeModel object that shares cells with the discretize
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tensor mesh and which stores the results of computations.
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:return mesh: The discretize tensor mesh object for computations.
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"""
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line_data = survey.get_entity("line_ids")[0]
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assert isinstance(line_data, IntegerData)
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lines = line_data.values
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entity, mesh, _ = get_drape_model( # pylint: disable=unbalanced-tuple-unpacking
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survey.workspace,
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name,
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survey.vertices[np.unique(survey.cells[lines == line_id, :]), :],
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[cell_size[0], cell_size[2]],
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100.0,
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[padding_distance] * 2 + [padding_distance] * 2,
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1.1,
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parent=None,
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return_colocated_mesh=True,
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return_sorting=True,
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)
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return entity

‎simpeg_drivers/utils/synthetics/models.py‎

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# '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
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# Copyright (c) 2025 Mira Geoscience Ltd. '
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# '
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# This file is part of simpeg-drivers package. '
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# '
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# simpeg-drivers is distributed under the terms and conditions of the MIT License '
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# (see LICENSE file at the root of this source code package). '
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# '
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# '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
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import numpy as np
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from geoapps_utils.modelling.plates import make_plate
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from geoh5py.data import FloatData
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from geoh5py.objects import DrapeModel, Octree
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from simpeg_drivers.utils.synthetics.options import ModelOptions
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18+
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def get_model(
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method: str,
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mesh: Octree | DrapeModel,
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active: np.ndarray,
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options: ModelOptions,
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) -> FloatData:
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"""
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Create a halfspace and plate model in the cell centers of the provided mesh.
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:param method: The geophysical method controlling the factory behaviour
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:param mesh: The mesh whose cell centers the model will be defined on.
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:param plate: The plate object defining the location and orientation of the
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plate anomaly.
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:param background: Value given to the halfspace.
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:param anomaly: Value given to the plate.
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"""
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cell_centers = mesh.centroids.copy()
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model = make_plate(
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points=cell_centers,
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plate=options.plate,
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background=options.background,
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anomaly=options.anomaly,
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)
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if "1d" in method:
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model = options.background * np.ones(mesh.n_cells)
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inside_anomaly = (mesh.centroids[:, 2] < 0) & (mesh.centroids[:, 2] > -20)
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model[inside_anomaly] = options.anomaly
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model[~active] = np.nan
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model = mesh.add_data({options.name: {"values": model}})
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assert isinstance(model, FloatData)
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return model

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