ogstools.meshlib package

class ogstools.meshlib.Surface

Bases: object

A surface is a sub group of a polygon mesh (2D). A surface is not closed and therefore does not represent a volume. (Geological) layers (stratigraphic units) can be defined by an upper and lower surface. By convention, properties (material_id and resolution ), actually associated to the stratigraphic unit layer, are given together with the lower boundary (class Surface) of a stratigraphic unit (class Layer).

Initialize a surface mesh. Either from pyvista or from a file.

property material_id: int

__init__(input, material_id)

Initialize a surface mesh. Either from pyvista or from a file.

Parameters:

• input (Path | DataSet) –

• material_id (int) –

create_raster_file(resolution)

Creates a raster file specific to resolution. If outfile is not specified, the extension is replaced by .asc

:returns the path and filename of the created file (.asc)

Parameters:

resolution (float) –

Return type:

Path

class ogstools.meshlib.Layer

Bases: Boundary

Layer(top: ogstools.meshlib.boundary_subset.Surface, bottom: ogstools.meshlib.boundary_subset.Surface, material_id: int = 0, num_subdivisions: int = 0)

top: Surface

bottom: Surface

material_id: int = 0

num_subdivisions: int = 0

Class representing a geological layer with top and bottom surfaces.

A geological layer is a distinct unit of rock or sediment that has unique properties and characteristics, associated by the material_id. It is often bounded by two surfaces: the top surface and the bottom surface. These surfaces delineate the spatial extent of the layer in the GIS system.

create_raster(resolution)

Create raster representations for the layer.

For each surface, including intermediate surfaces (num_of_subdivisions > 0), this method generates .asc files.

Args:

resolution (float): The resolution for raster creation.

Returns:

list[Path]: A list of filenames to .asc raster files.

Parameters:

resolution (float) –

Return type:

list[Path]

dim()

Get the dimension of the boundary.

Returns:

int: The dimension of the boundary. For example, the dimension of a boundary of a cube (3D) is 2.

__init__(top, bottom, material_id=0, num_subdivisions=0)

Parameters:

• top (Surface) –

• bottom (Surface) –

• material_id (int) –

• num_subdivisions (int) –

Return type:

None

class ogstools.meshlib.Raster

Bases: object

Class representing a raster representation of a location frame.

This class provides methods to create and save a raster representation based on a specified location frame and resolution.

frame: LocationFrame

resolution: float

__init__(frame, resolution)

Parameters:

• frame (LocationFrame) –

• resolution (float) –

Return type:

None

as_vtu(outfilevtu)

Create and save a raster representation as a VTK unstructured grid.

Args:

outfilevtu (Path): The path to save the VTK unstructured grid representation.

Returns:

Path: The path to the saved VTK unstructured grid representation.

Parameters:

outfilevtu (Path) –

Return type:

Path

class ogstools.meshlib.LocationFrame

Bases: object

LocationFrame(xmin: float, xmax: float, ymin: float, ymax: float)

xmin: float

xmax: float

ymin: float

ymax: float

as_gml(filename)

Generate GML representation of the location frame.

Args:

filename (Path): The filename to save the GML representation to.

Returns:

None

Parameters:

filename (Path) –

__init__(xmin, xmax, ymin, ymax)

Parameters:

• xmin (float) –

• xmax (float) –

• ymin (float) –

• ymax (float) –

Return type:

None

class ogstools.meshlib.Boundary

Bases: ABC

Abstract base class representing a boundary within a mesh.

A boundary refers to the set of edges or faces that defines the delineation between the interior region and exterior regions of a mesh. In a 2D mesh, it is formed by a closed collection of line segments (1D). In a 3D mesh, it is formed by a closed collection of faces (2D).

abstract dim()

Get the dimension of the boundary.

Returns:

int: The dimension of the boundary. For example, the dimension of a boundary of a cube (3D) is 2.

class ogstools.meshlib.MeshSeries

Bases: object

A wrapper around pyvista and meshio for reading of pvd and xdmf timeseries.

Will be replaced by own module in ogstools with similar interface.

__init__(filepath)

Parameters:

filepath (str | Path) –

Return type:

None

read(timestep, lazy_eval=True)

Lazy read function.

Parameters:

• timestep (int) –

• lazy_eval (bool) –

Return type:

UnstructuredGrid

clear()

Return type:

None

property timesteps: range

Return the timesteps of the timeseries data.

property timevalues: list[float]

Return the timevalues of the timeseries data.

closest_timestep(timevalue)

Return the corresponding timestep from a timevalue.

Parameters:

timevalue (float) –

Return type:

int

closest_timevalue(timevalue)

Return the closest timevalue to a timevalue.

Parameters:

timevalue (float) –

Return type:

float

read_closest(timevalue)

Return the closest timestep in the data for a given timevalue.

Parameters:

timevalue (float) –

Return type:

UnstructuredGrid

read_interp(timevalue, lazy_eval=True)

Return the temporal interpolated mesh for a given timevalue.

Parameters:

• timevalue (float) –

• lazy_eval (bool) –

Return type:

UnstructuredGrid

class ogstools.meshlib.LayerSet

Bases: BoundarySet

Collection of geological layers stacked to represent subsurface arrangements.

In a geological information system, multiple layers can be stacked vertically to represent the subsurface arrangement. This class provides methods to manage and work with layered geological data.

Initializes a LayerSet. It checks if the list of provided layers are given in a top to bottom order. In neighboring layers, layers share the same surface (upper bottom == low top).

__init__(layers)

Initializes a LayerSet. It checks if the list of provided layers are given in a top to bottom order. In neighboring layers, layers share the same surface (upper bottom == low top).

Parameters:

layers (list[Layer]) –

bounds()

filenames()

classmethod from_pandas(df)

Create a LayerSet from a Pandas DataFrame.

Parameters:

df (DataFrame) –

create_raster(resolution)

Create raster representations for the LayerSet.

This method generates raster files at a specified resolution for each layer’s top and bottom boundaries and returns paths to the raster files.

create_rasters(resolution)

For each surface a (temporary) raster file with given resolution is created.

Parameters:

resolution (int) –

Return type:

list[Path]

ogstools.meshlib.rect(lengths=1.0, n_edge_cells=1, structured_grid=True, order=1, out_name=Path('unit_square.msh'))

Parameters:

• lengths (float | list[float]) –

• n_edge_cells (int | list[int]) –

• structured_grid (bool) –

• order (int) –

• out_name (Path) –

ogstools.meshlib.cuboid(lengths=1.0, n_edge_cells=1, structured_grid=True, order=1, out_name=Path('unit_cube.msh'))

Parameters:

• lengths (float | list[float]) –

• n_edge_cells (int | list[int]) –

• structured_grid (bool) –

• order (int) –

• out_name (Path) –

Subpackages

• ogstools.meshlib.region package
  • to_region_prism()
  • to_region_simplified()
  • to_region_tetraeder()
  • to_region_voxel()
  • RegionSet
    • RegionSet.__init__()
    • RegionSet.box_boundaries()
  • to_boundary()
  • Submodules
    • ogstools.meshlib.region.region module
      • RegionSet
      • to_boundary()
      • to_region_prism()
      • layer_to_simplified_mesh()
      • to_region_simplified()
      • to_region_tetraeder()
      • to_region_voxel()

Submodules

• ogstools.meshlib.boundary module
  • Boundary
    • Boundary.dim()
  • Layer
    • Layer.top
    • Layer.bottom
    • Layer.material_id
    • Layer.num_subdivisions
    • Layer.create_raster()
    • Layer.dim()
    • Layer.__init__()
  • LocationFrame
    • LocationFrame.xmin
    • LocationFrame.xmax
    • LocationFrame.ymin
    • LocationFrame.ymax
    • LocationFrame.as_gml()
    • LocationFrame.__init__()
  • Raster
    • Raster.frame
    • Raster.resolution
    • Raster.__init__()
    • Raster.as_vtu()
• ogstools.meshlib.boundary_set module
  • BoundarySet
    • BoundarySet.bounds()
    • BoundarySet.filenames()
  • LayerSet
    • LayerSet.__init__()
    • LayerSet.bounds()
    • LayerSet.filenames()
    • LayerSet.from_pandas()
    • LayerSet.create_raster()
    • LayerSet.create_rasters()
• ogstools.meshlib.boundary_subset module
  • Surface
    • Surface.material_id
    • Surface.__init__()
    • Surface.create_raster_file()
  • Gaussian2D()
• ogstools.meshlib.gmsh_meshing module
  • rect()
  • cuboid()
• ogstools.meshlib.mesh_series module
  • TimeSeriesReader
    • TimeSeriesReader.__init__()
    • TimeSeriesReader.read_data()
  • MeshSeries
    • MeshSeries.__init__()
    • MeshSeries.read()
    • MeshSeries.clear()
    • MeshSeries.timesteps
    • MeshSeries.timevalues
    • MeshSeries.closest_timestep()
    • MeshSeries.closest_timevalue()
    • MeshSeries.read_closest()
    • MeshSeries.read_interp()
• ogstools.meshlib.refine_mesh module
  • refine()