PyHydroGeophysX.core package

Submodules

PyHydroGeophysX.core.interpolation module

Interpolation utilities for geophysical data processing.

class PyHydroGeophysX.core.interpolation.ProfileInterpolator(point1: List[int], point2: List[int], surface_data: ndarray, origin_x: float = 0.0, origin_y: float = 0.0, pixel_width: float = 1.0, pixel_height: float = -1.0, num_points: int = 200)

Bases: object

Class for handling interpolation of data to/from profiles.

interpolate_3d_data(data: ndarray) → ndarray

Interpolate 3D data (n_layers, ny, nx) to profile.

Parameters:

data – 3D array of values

Returns:

Array of interpolated values (n_layers, n_profile_points)

interpolate_layer_data(layer_data: List[ndarray]) → ndarray

Interpolate multiple layer data to profile.

Parameters:

layer_data – List of 2D arrays for each layer

Returns:

Array of interpolated values (n_layers, n_profile_points)

interpolate_to_mesh(property_values: ndarray, depth_values: ndarray, mesh_x: ndarray, mesh_y: ndarray, mesh_markers: ndarray, ID: ndarray, layer_markers: list = [3, 0, 2]) → ndarray

Interpolate property values from profile to mesh with layer-specific handling.

Parameters:

• property_values – Property values array (n_points or n_layers, n_points)

• depth_values – Depth values array (n_layers, n_points)

• mesh_x – Coordinates of mesh cells

• mesh_y – Coordinates of mesh cells

• mesh_markers – Markers indicating different layers in mesh

• layer_markers – List of marker values for each layer

Returns:

Interpolated values for mesh cells

PyHydroGeophysX.core.interpolation.create_surface_lines(L_profile: ndarray, structure: ndarray, top_idx: int = 0, mid_idx: int = 4, bot_idx: int = 12) → Tuple[ndarray, ndarray, ndarray]

Create surface and boundary lines from structure data

Parameters:

• L_profile – Distance along profile

• structure – Interpolated structure data

• top_idx – Index for top surface

• mid_idx – Index for middle boundary

• bot_idx – Index for bottom boundary

Returns:

Surface coordinates line1: First boundary coordinates line2: Second boundary coordinates

Return type:

surface

PyHydroGeophysX.core.interpolation.interpolate_structure_to_profile(structure_data: List[ndarray], X_grid: ndarray, Y_grid: ndarray, X_pro: ndarray, Y_pro: ndarray) → ndarray

Interpolate multiple structure layers onto profile

Parameters:

• structure_data – List of 2D arrays for each layer

• X_grid – X coordinates of original grid

• Y_grid – Y coordinates of original grid

• X_pro – X coordinates of profile points

• Y_pro – Y coordinates of profile points

Returns:

Array of interpolated values with shape (n_layers, n_points)

PyHydroGeophysX.core.interpolation.interpolate_to_mesh(property_values: ndarray, profile_distance: ndarray, depth_values: ndarray, mesh_x: ndarray, mesh_y: ndarray, mesh_markers: ndarray, ID, layer_markers: list = [3, 0, 2]) → ndarray

Interpolate property values from profile to mesh with layer-specific handling.

Parameters:

• property_values – Property values array (n_points)

• profile_distance – Distance along profile (n_points)

• depth_values – Depth values array (n_layers, n_points)

• mesh_x – X coordinates of mesh cells

• mesh_y – Y coordinates of mesh cells

• mesh_markers – Markers indicating different layers in mesh

• layer_markers – List of marker values for each layer

Returns:

Interpolated values for mesh cells

PyHydroGeophysX.core.interpolation.interpolate_to_profile(data: ndarray, X_grid: ndarray, Y_grid: ndarray, X_pro: ndarray, Y_pro: ndarray, method: str = 'linear') → ndarray

Interpolate 2D data onto a profile line

Parameters:

• data – 2D array of values to interpolate

• X_grid – X coordinates of original grid (meshgrid)

• Y_grid – Y coordinates of original grid (meshgrid)

• X_pro – X coordinates of profile points

• Y_pro – Y coordinates of profile points

• method – Interpolation method (‘linear’ or ‘nearest’)

Returns:

Interpolated values along profile

PyHydroGeophysX.core.interpolation.prepare_2D_profile_data(data: ndarray, XX: ndarray, YY: ndarray, X_pro: ndarray, Y_pro: ndarray) → ndarray

Interpolate multiple 2D gridded data layers onto a profile line.

Parameters:

• data – 3D array of gridded data (n_layers, ny, nx)

• XX – Coordinate grids from meshgrid

• YY – Coordinate grids from meshgrid

• X_pro – Profile line coordinates

• Y_pro – Profile line coordinates

Returns:

Interpolated values along profile (n_layers, n_profile_points)

PyHydroGeophysX.core.interpolation.setup_profile_coordinates(point1: List[int], point2: List[int], surface_data: ndarray, origin_x: float = 0.0, origin_y: float = 0.0, pixel_width: float = 1.0, pixel_height: float = -1.0, num_points: int = 200) → Tuple[ndarray, ndarray, ndarray, ndarray, ndarray]

Set up profile coordinates based on surface elevation data between two points

Parameters:

• point1 – Starting point indices [col, row]

• point2 – Ending point indices [col, row]

• surface_data – 2D array of surface elevation data

• origin_x – X coordinate of origin

• origin_y – Y coordinate of origin

• pixel_width – Width of each pixel

• pixel_height – Height of each pixel (negative for top-down)

• num_points – Number of points along profile

Returns:

X coordinates along profile Y_pro: Y coordinates along profile L_profile: Distances along profile XX: X coordinate grid YY: Y coordinate grid

Return type:

X_pro

PyHydroGeophysX.core.kriging_3d module

PyHydroGeophysX.core.mesh_utils module

Mesh utilities for geophysical modeling and inversion.

class PyHydroGeophysX.core.mesh_utils.MeshCreator(quality: float = 28, area: float = 40)

Bases: object

Class for creating and managing meshes for geophysical inversion.

create_from_ert_data(data, max_depth: float = 30.0, quality: float = 34)

Create a mesh suitable for ERT inversion from ERT data.

Parameters:

• data – PyGIMLI ERT data object

• max_depth – Maximum depth of the mesh

• quality – Mesh quality parameter

Returns:

PyGIMLI mesh for ERT inversion

create_from_layers(surface: ndarray, layers: List[ndarray], bottom_depth: float = 30.0, markers: List[int] | None = None) → pygimli.Mesh

Create a mesh from surface and layer boundaries.

Parameters:

• surface – Surface coordinates [[x,z],…]

• layers – List of layer boundary coordinates

• bottom_depth – Depth below surface minimum for mesh bottom

• markers – List of markers for each layer (default: [2, 3, 2, …])

Returns:

PyGIMLI mesh

PyHydroGeophysX.core.mesh_utils.add_velocity_interface(ertData, smooth_x, smooth_z, paraBoundary=2, boundary=1)

Add a velocity interface line to the geometry and create a mesh with different markers: - Outside survey area: marker = 1 - Inside survey area, above velocity line: marker = 2 - Inside survey area, below velocity line: marker = 3

Parameters:

• ertData – ERT data with sensor positions

• smooth_x – Arrays with x and z coordinates of the velocity interface

• smooth_z – Arrays with x and z coordinates of the velocity interface

• paraBoundary – Parameter boundary size (default: 2)

• boundary – Boundary marker (default: 1)

Returns:

Array with cell markers meshafter: The created mesh with updated markers

Return type:

markers

PyHydroGeophysX.core.mesh_utils.createTriangles(mesh)

Generate triangle objects for later drawing.

Creates triangle for each 2D triangle cell or 3D boundary. Quads will be split into two triangles. Result will be cached into mesh._triData.

Parameters:

mesh (:gimliapi:`GIMLI::Mesh`) – 2D mesh or 3D mesh

Returns:

• x (numpy array) – x position of nodes

• y (numpy array) – x position of nodes

• triangles (numpy array Cx3) – cell indices for each triangle, quad or boundary face

• z (numpy array) – z position for given indices

• dataIdx (list of int) – List of indices for a data array

PyHydroGeophysX.core.mesh_utils.create_mesh_from_layers(surface: ndarray, line1: ndarray, line2: ndarray, bottom_depth: float = 30.0, quality: float = 28, area: float = 40) → Tuple[pygimli.Mesh, ndarray, ndarray]

Create mesh from layer boundaries and get cell centers and markers.

Parameters:

• surface – Surface coordinates [[x,z],…]

• line1 – First layer boundary coordinates

• line2 – Second layer boundary coordinates

• bottom_depth – Depth below surface minimum for mesh bottom

• quality – Mesh quality parameter

• area – Maximum cell area

Returns:

PyGIMLI mesh mesh_centers: Array of cell center coordinates markers: Array of cell markers

Return type:

mesh

PyHydroGeophysX.core.mesh_utils.extract_velocity_interface(mesh, velocity_data, threshold=1200, interval=4.0, x_min=None, x_max=None)

Extract the interface where velocity equals the threshold value.

Parameters: mesh - The PyGIMLi mesh velocity_data - The velocity values threshold - The velocity value defining the interface (default: 1200) interval - The binning interval for extracting the interface (default: 4.0) x_min - Optional: minimum x-coordinate for the range (default: None, uses mesh data) x_max - Optional: maximum x-coordinate for the range (default: None, uses mesh data)

Returns: x_dense, z_dense - Arrays with x and z coordinates of the smooth interface

PyHydroGeophysX.core.mesh_utils.fill_holes_2d(pos, cov, grid_resolution=100)

Fill holes (0 values) surrounded by 1 values in 2D scattered data.

Parameters:

posndarray of shape (n, 3)

Position array where first two columns are x,y coordinates

covndarray of shape (n,)

Coverage values at each point (0 or 1)

grid_resolutionint

Resolution of the grid for interpolation

Returns:

filled_covndarray of shape (n,)

Updated coverage values with holes filled

PyHydroGeophysX.core.plt_utils module

Plotting utilities for PyHydroGeophysX.

PyHydroGeophysX.core.plt_utils.drawFirstPicks(ax, data, tt=None, plotva=False, **kwargs)

Plot first arrivals as lines.

Parameters:

• ax (matplotlib.axes) – axis to draw the lines in

• data (:gimliapi:`GIMLI::DataContainer`) – data containing shots (“s”), geophones (“g”) and traveltimes (“t”)

• tt (array, optional) – traveltimes to use instead of data(“t”)

• plotva (bool, optional) – plot apparent velocity instead of traveltimes

Returns:

ax – the modified axis

Return type:

matplotlib.axes

Module contents

Core utilities for geophysical modeling and inversion.

class PyHydroGeophysX.core.MeshCreator(quality: float = 28, area: float = 40)

Bases: object

Class for creating and managing meshes for geophysical inversion.

create_from_ert_data(data, max_depth: float = 30.0, quality: float = 34)

Create a mesh suitable for ERT inversion from ERT data.

Parameters:

• data – PyGIMLI ERT data object

• max_depth – Maximum depth of the mesh

• quality – Mesh quality parameter

Returns:

PyGIMLI mesh for ERT inversion

create_from_layers(surface: ndarray, layers: List[ndarray], bottom_depth: float = 30.0, markers: List[int] | None = None) → pygimli.Mesh

Create a mesh from surface and layer boundaries.

Parameters:

• surface – Surface coordinates [[x,z],…]

• layers – List of layer boundary coordinates

• bottom_depth – Depth below surface minimum for mesh bottom

• markers – List of markers for each layer (default: [2, 3, 2, …])

Returns:

PyGIMLI mesh

class PyHydroGeophysX.core.ProfileInterpolator(point1: List[int], point2: List[int], surface_data: ndarray, origin_x: float = 0.0, origin_y: float = 0.0, pixel_width: float = 1.0, pixel_height: float = -1.0, num_points: int = 200)

Bases: object

Class for handling interpolation of data to/from profiles.

interpolate_3d_data(data: ndarray) → ndarray

Interpolate 3D data (n_layers, ny, nx) to profile.

Parameters:

data – 3D array of values

Returns:

Array of interpolated values (n_layers, n_profile_points)

interpolate_layer_data(layer_data: List[ndarray]) → ndarray

Interpolate multiple layer data to profile.

Parameters:

layer_data – List of 2D arrays for each layer

Returns:

Array of interpolated values (n_layers, n_profile_points)

interpolate_to_mesh(property_values: ndarray, depth_values: ndarray, mesh_x: ndarray, mesh_y: ndarray, mesh_markers: ndarray, ID: ndarray, layer_markers: list = [3, 0, 2]) → ndarray

Interpolate property values from profile to mesh with layer-specific handling.

Parameters:

• property_values – Property values array (n_points or n_layers, n_points)

• depth_values – Depth values array (n_layers, n_points)

• mesh_x – Coordinates of mesh cells

• mesh_y – Coordinates of mesh cells

• mesh_markers – Markers indicating different layers in mesh

• layer_markers – List of marker values for each layer

Returns:

Interpolated values for mesh cells

PyHydroGeophysX.core.add_velocity_interface(ertData, smooth_x, smooth_z, paraBoundary=2, boundary=1)

Add a velocity interface line to the geometry and create a mesh with different markers: - Outside survey area: marker = 1 - Inside survey area, above velocity line: marker = 2 - Inside survey area, below velocity line: marker = 3

Parameters:

• ertData – ERT data with sensor positions

• smooth_x – Arrays with x and z coordinates of the velocity interface

• smooth_z – Arrays with x and z coordinates of the velocity interface

• paraBoundary – Parameter boundary size (default: 2)

• boundary – Boundary marker (default: 1)

Returns:

Array with cell markers meshafter: The created mesh with updated markers

Return type:

markers

PyHydroGeophysX.core.create_mesh_from_layers(surface: ndarray, line1: ndarray, line2: ndarray, bottom_depth: float = 30.0, quality: float = 28, area: float = 40) → Tuple[pygimli.Mesh, ndarray, ndarray]

Create mesh from layer boundaries and get cell centers and markers.

Parameters:

• surface – Surface coordinates [[x,z],…]

• line1 – First layer boundary coordinates

• line2 – Second layer boundary coordinates

• bottom_depth – Depth below surface minimum for mesh bottom

• quality – Mesh quality parameter

• area – Maximum cell area

Returns:

PyGIMLI mesh mesh_centers: Array of cell center coordinates markers: Array of cell markers

Return type:

mesh

PyHydroGeophysX.core.create_surface_lines(L_profile: ndarray, structure: ndarray, top_idx: int = 0, mid_idx: int = 4, bot_idx: int = 12) → Tuple[ndarray, ndarray, ndarray]

Create surface and boundary lines from structure data

Parameters:

• L_profile – Distance along profile

• structure – Interpolated structure data

• top_idx – Index for top surface

• mid_idx – Index for middle boundary

• bot_idx – Index for bottom boundary

Returns:

Surface coordinates line1: First boundary coordinates line2: Second boundary coordinates

Return type:

surface

PyHydroGeophysX.core.extract_velocity_interface(mesh, velocity_data, threshold=1200, interval=4.0, x_min=None, x_max=None)

Extract the interface where velocity equals the threshold value.

Parameters: mesh - The PyGIMLi mesh velocity_data - The velocity values threshold - The velocity value defining the interface (default: 1200) interval - The binning interval for extracting the interface (default: 4.0) x_min - Optional: minimum x-coordinate for the range (default: None, uses mesh data) x_max - Optional: maximum x-coordinate for the range (default: None, uses mesh data)

Returns: x_dense, z_dense - Arrays with x and z coordinates of the smooth interface

PyHydroGeophysX.core.interpolate_structure_to_profile(structure_data: List[ndarray], X_grid: ndarray, Y_grid: ndarray, X_pro: ndarray, Y_pro: ndarray) → ndarray

Interpolate multiple structure layers onto profile

Parameters:

• structure_data – List of 2D arrays for each layer

• X_grid – X coordinates of original grid

• Y_grid – Y coordinates of original grid

• X_pro – X coordinates of profile points

• Y_pro – Y coordinates of profile points

Returns:

Array of interpolated values with shape (n_layers, n_points)

PyHydroGeophysX.core.interpolate_to_mesh(property_values: ndarray, profile_distance: ndarray, depth_values: ndarray, mesh_x: ndarray, mesh_y: ndarray, mesh_markers: ndarray, ID, layer_markers: list = [3, 0, 2]) → ndarray

Interpolate property values from profile to mesh with layer-specific handling.

Parameters:

• property_values – Property values array (n_points)

• profile_distance – Distance along profile (n_points)

• depth_values – Depth values array (n_layers, n_points)

• mesh_x – X coordinates of mesh cells

• mesh_y – Y coordinates of mesh cells

• mesh_markers – Markers indicating different layers in mesh

• layer_markers – List of marker values for each layer

Returns:

Interpolated values for mesh cells

PyHydroGeophysX.core.interpolate_to_profile(data: ndarray, X_grid: ndarray, Y_grid: ndarray, X_pro: ndarray, Y_pro: ndarray, method: str = 'linear') → ndarray

Interpolate 2D data onto a profile line

Parameters:

• data – 2D array of values to interpolate

• X_grid – X coordinates of original grid (meshgrid)

• Y_grid – Y coordinates of original grid (meshgrid)

• X_pro – X coordinates of profile points

• Y_pro – Y coordinates of profile points

• method – Interpolation method (‘linear’ or ‘nearest’)

Returns:

Interpolated values along profile

PyHydroGeophysX.core.prepare_2D_profile_data(data: ndarray, XX: ndarray, YY: ndarray, X_pro: ndarray, Y_pro: ndarray) → ndarray

Interpolate multiple 2D gridded data layers onto a profile line.

Parameters:

• data – 3D array of gridded data (n_layers, ny, nx)

• XX – Coordinate grids from meshgrid

• YY – Coordinate grids from meshgrid

• X_pro – Profile line coordinates

• Y_pro – Profile line coordinates

Returns:

Interpolated values along profile (n_layers, n_profile_points)

PyHydroGeophysX.core.setup_profile_coordinates(point1: List[int], point2: List[int], surface_data: ndarray, origin_x: float = 0.0, origin_y: float = 0.0, pixel_width: float = 1.0, pixel_height: float = -1.0, num_points: int = 200) → Tuple[ndarray, ndarray, ndarray, ndarray, ndarray]

Set up profile coordinates based on surface elevation data between two points

Parameters:

• point1 – Starting point indices [col, row]

• point2 – Ending point indices [col, row]

• surface_data – 2D array of surface elevation data

• origin_x – X coordinate of origin

• origin_y – Y coordinate of origin

• pixel_width – Width of each pixel

• pixel_height – Height of each pixel (negative for top-down)

• num_points – Number of points along profile

Returns:

X coordinates along profile Y_pro: Y coordinates along profile L_profile: Distances along profile XX: X coordinate grid YY: Y coordinate grid

Return type:

X_pro