subsurface-terra 2025.1.0rc11__tar.gz → 2025.1.0rc13__tar.gz

{subsurface_terra-2025.1.0rc11 → subsurface_terra-2025.1.0rc13}/.teamcity/Subsurface/buildTypes/Subsurface_Testing.xml

@@ -1,8 +1,11 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<build-type xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" uuid="ed495f4f-4df2-4a37-bbfe-2489430a46e8" xsi:noNamespaceSchemaLocation="https://www.jetbrains.com/teamcity/schemas/2021.1/project-config.xsd">
+<build-type xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" uuid="ed495f4f-4df2-4a37-bbfe-2489430a46e8" xsi:noNamespaceSchemaLocation="https://www.jetbrains.com/teamcity/schemas/2025.3/project-config.xsd">
   <name>Testing</name>
   <description />
   <settings>
+    <options>
+      <option name="shouldFailBuildOnBadExitCode" value="false" />
+    </options>
     <parameters>
       <param name="REQUIREMENT_LEVEL" value="READ_MESH" />
       <param name="env.MPLBACKEND" value="Agg" />
@@ -11,6 +14,9 @@
       <param name="env.PATH_TO_BOLIDEN" value="%env.TERRA_PATH_DEVOPS%/combined/Leapfrog_OMF/Garpenberg_global_20220715.omf" />
       <param name="env.PATH_TO_GLB" value="%env.TERRA_PATH_DEVOPS%/meshes/GLB - GLTF/Duck.glb" />
       <param name="env.PATH_TO_GLB_COMPLEX" value="%env.TERRA_PATH_DEVOPS%/meshes/GLB - GLTF/GlbFile.glb" />
+      <param name="env.PATH_TO_GRAV3D_MOD" value="%env.TERRA_PATH_DEVOPS%/volume/MSH/19_simpeg_inv_result_25ft_7.62m_psi2_Sep.mod" />
+      <param name="env.PATH_TO_GRAV3D_MSH" value="%env.TERRA_PATH_DEVOPS%/volume/MSH/client_voxel.msh" />
+      <param name="env.PATH_TO_GRAV3D_MSH_II" value="%env.TERRA_PATH_DEVOPS%/volume/MSH/IDN-65/ubc_mesh_mod" />
       <param name="env.PATH_TO_INTERPRETATION" value="%env.TERRA_PATH_DEVOPS%/meshes/Seismic/Anl2-1.tif" />
       <param name="env.PATH_TO_MAGNETIC_INTERPRETATION" value="%env.TERRA_PATH_DEVOPS%/meshes/Magnetic/Plate 2a - Profile 1 2D inversion.pdf" />
       <param name="env.PATH_TO_MTL" value="%env.TERRA_PATH_DEVOPS%/meshes/OBJ/Broadhaven_Obj/model/model.mtl" />
@@ -89,7 +95,6 @@ venv\Scripts\python -m pytest --teamcity -v]]></param>
     <vcs-settings>
       <vcs-entry-ref root-id="Subsurface_HttpsGithubComTerranigmaSolutionsSubsurfaceRefsHeadsMain2" />
     </vcs-settings>
-    <requirements />
     <build-triggers>
       <build-trigger id="TRIGGER_4" type="vcsTrigger">
         <parameters>
@@ -123,7 +128,6 @@ venv\Scripts\python -m pytest --teamcity -v]]></param>
         </parameters>
       </extension>
     </build-extensions>
-    <cleanup />
   </settings>
 </build-type>
 

{subsurface_terra-2025.1.0rc11/subsurface_terra.egg-info → subsurface_terra-2025.1.0rc13}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: subsurface_terra
-Version: 2025.1.0rc11
+Version: 2025.1.0rc13
 Summary: Subsurface data types and utilities. This version is the one used by Terranigma Solutions. Please feel free to take anything in this repository for the original one.
 Home-page: https://softwareunderground.github.io/subsurface
 Author: Software Underground

{subsurface_terra-2025.1.0rc11 → subsurface_terra-2025.1.0rc13}/subsurface/_version.py

@@ -17,5 +17,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '2025.1.0rc11'
-__version_tuple__ = version_tuple = (2025, 1, 0)
+__version__ = version = '2025.1.0rc13'
+__version_tuple__ = version_tuple = (2025, 1, 0, 'rc13')

{subsurface_terra-2025.1.0rc11 → subsurface_terra-2025.1.0rc13}/subsurface/api/__init__.py

@@ -8,5 +8,6 @@ from .interfaces.stream import (
     VTK_stream_to_struct,  
     MX_stream_to_unstruc,
     OBJ_stream_to_trisurf,
-    GLTF_stream_to_trisurf
+    GLTF_stream_to_trisurf,
+    MSH_stream_to_struct,
 )

{subsurface_terra-2025.1.0rc11 → subsurface_terra-2025.1.0rc13}/subsurface/api/interfaces/stream.py

@@ -1,6 +1,6 @@
 import io
 from io import BytesIO
-from typing import TextIO
+from typing import TextIO, Optional
 
 import pandas
 
@@ -57,11 +57,17 @@ def GLTF_stream_to_trisurf(gltf_stream: io.BytesIO, coordinate_system: TriMeshTr
     tri_mesh: TriSurf = reader.load_gltf_with_trimesh(gltf_stream, coordinate_system)
     return tri_mesh
 
+
 def VTK_stream_to_struct(stream: BytesIO, attribute_name: str) -> list[StructuredData]:
     struct = read_VTK_structured_grid(stream, attribute_name)
     return [struct]
 
 
+def MSH_stream_to_struct(grid_stream: TextIO, values_stream: TextIO, missing_value: Optional[float], attr_name: Optional[str]) -> list[StructuredData]:
+    struct = reader.read_msh_structured_grid(grid_stream, values_stream, missing_value, attr_name)
+    return [struct]
+
+
 def CSV_wells_stream_to_unstruc(
         collars_reader: GenericReaderFilesHelper,
         surveys_reader: GenericReaderFilesHelper,

{subsurface_terra-2025.1.0rc11 → subsurface_terra-2025.1.0rc13}/subsurface/core/structs/base_structures/structured_data.py

@@ -131,12 +131,29 @@ class StructuredData:
     def values(self) -> np.ndarray:
         return self.data[self.active_data_array_name].values
 
+    _bounds: Tuple[float, float, float, float, float, float] = None
+
     @property
     def bounds(self):
+        if self._bounds is not None:
+            return self._bounds
+
         array_: xr.DataArray = self.data[self.active_data_array_name]
-        bounds = self._get_bounds(array_)
+        bounds = self._get_bounds_from_coord(array_)
         return bounds
 
+    @bounds.setter
+    def bounds(self, bounds: Tuple[float, float, float, float, float, float]):
+        """
+        Set the bounds of the structured data. This is useful for defining the
+        spatial extent of the data in a structured grid.
+
+        Args:
+            bounds (Tuple[float, float, float, float, float, float]): A tuple containing
+                the minimum and maximum values for each dimension (xmin, xmax, ymin, ymax, zmin, zmax).
+        """
+        self._bounds = bounds
+
     @property
     def shape(self):
         return self.active_data_array.shape
@@ -146,7 +163,7 @@ class StructuredData:
         return self.data[self.active_data_array_name]
 
     @staticmethod
-    def _get_bounds(xr_obj: xr.DataArray):
+    def _get_bounds_from_coord(xr_obj: xr.DataArray):
         bounds = {}
         for coord in xr_obj.coords:
             bounds[coord] = (xr_obj[coord].min().item(), xr_obj[coord].max().item())

{subsurface_terra-2025.1.0rc11 → subsurface_terra-2025.1.0rc13}/subsurface/core/structs/structured_elements/structured_grid.py

@@ -33,6 +33,10 @@ class StructuredGrid:
         grid_3d = np.meshgrid(*cart_coord, indexing='ij')
         return grid_3d
 
+    @property
+    def active_attributes(self) -> np.ndarray:
+        return self.ds.data[self.ds.active_data_array_name].values
+
     def meshgrid_2d(self, attribute_name_coord_name: str = None) -> list:
         """
 

{subsurface_terra-2025.1.0rc11 → subsurface_terra-2025.1.0rc13}/subsurface/modules/reader/__init__.py

@@ -9,3 +9,5 @@ from .mesh.dxf_reader import dxf_stream_to_unstruct_input, dxf_file_to_unstruct_
 from .mesh.mx_reader import mx_to_unstruc_from_binary
 from .mesh.obj_reader import load_obj_with_trimesh, load_obj_with_trimesh_from_binary
 from .mesh.glb_reader import load_gltf_with_trimesh
+
+from .volume.read_grav3d import read_msh_structured_grid

{subsurface_terra-2025.1.0rc11 → subsurface_terra-2025.1.0rc13}/subsurface/modules/reader/mesh/_trimesh_reader.py

@@ -9,9 +9,14 @@ from .... import optional_requirements
 from ....core.structs import TriSurf, StructuredData
 
 
-class TriMeshTransformations(enum.Enum):
-    RIGHT_HANDED_Z_UP = "right_handed_z_up"
-    ORIGINAL = "original"
+class TriMeshTransformations(enum.Flag):
+    UP_Z = 2**1
+    UP_Y = 2**2
+    FORWARD_MINUS_Z = 2**3
+    FORWARD_PLUS_Z = 2**4
+    RIGHT_HANDED_Z_UP_Y_REVERSED = UP_Y | FORWARD_MINUS_Z
+    RIGHT_HANDED_Z_UP = UP_Y | FORWARD_PLUS_Z
+    ORIGINAL = UP_Z | FORWARD_MINUS_Z
 
 
 def load_with_trimesh(path_to_file_or_buffer, file_type: Optional[str] = None,
@@ -23,13 +28,10 @@ def load_with_trimesh(path_to_file_or_buffer, file_type: Optional[str] = None,
     trimesh = optional_requirements.require_trimesh()
     scene_or_mesh = LoadWithTrimesh.load_with_trimesh(path_to_file_or_buffer, file_type, plot)
 
-    # Compute a -90° rotation around the X axis
-    angle_rad = np.deg2rad(-90)
-    transform = trimesh.transformations.rotation_matrix(angle_rad, [1, 0, 0])
-    
     match coordinate_system:
         case TriMeshTransformations.ORIGINAL:
             return scene_or_mesh
+        # * Forward -Z up Y
         case TriMeshTransformations.RIGHT_HANDED_Z_UP:
             # Transform from Y-up (modeling software) to Z-up (scientific)
             # This rotates the model so that:
@@ -42,16 +44,24 @@ def load_with_trimesh(path_to_file_or_buffer, file_type: Optional[str] = None,
                     [0, 1, 0, 0], 
                     [0, 0, 0, 1]
             ])
-
+        case TriMeshTransformations.RIGHT_HANDED_Z_UP_Y_REVERSED:
+            # * Forward Z Up Y
+            transform=np.array([
+                    [-1, 0, 0, 0],
+                    [0, 0, 1, 0],
+                    [0, 1, 0, 0],
+                    [0, 0, 0, 1],
+            ])
             # Apply the coordinate transformation
-            if isinstance(scene_or_mesh, trimesh.Scene):
-                for geometry in scene_or_mesh.geometry.values():
-                    geometry.apply_transform(transform)
-            else:
-                scene_or_mesh.apply_transform(transform)
+        # TODO: Add all the options of blender
         case _:
             raise ValueError(f"Invalid coordinate system: {coordinate_system}")
 
+    if isinstance(scene_or_mesh, trimesh.Scene):
+        for geometry in scene_or_mesh.geometry.values():
+            geometry.apply_transform(transform)
+    else:
+        scene_or_mesh.apply_transform(transform)
     return scene_or_mesh
 
 
@@ -99,6 +109,10 @@ class LoadWithTrimesh:
             # If there's already an image reference in the material, let the user know
             if hasattr(material, 'image') and material.image is not None:
                 print("  -> Material already has an image:", material.image)
+            
+            if geometry.visual.uv is None:
+                raise ValueError("Geometry does not have UV coordinates for texture mapping, despite having a material."
+                                 "This can also happen if the geometry is given in quads instead of triangles.")
         else:
             print("No material found or no 'material' attribute on this geometry.")
 

subsurface_terra-2025.1.0rc13/subsurface/modules/reader/volume/read_grav3d.py

@@ -0,0 +1,428 @@
+from dataclasses import dataclass, field
+from typing import List, Dict, Any, Tuple, Optional, Union, TextIO
+import numpy as np
+import xarray as xr
+from pathlib import Path
+
+from ....core.structs import StructuredData
+
+
+@dataclass
+class GridDimensions:
+    """
+    Represents the dimensions of a 3D grid.
+
+    Attributes:
+        nx (int): Number of cells in the x-direction
+        ny (int): Number of cells in the y-direction
+        nz (int): Number of cells in the z-direction
+    """
+    nx: int
+    ny: int
+    nz: int
+
+
+@dataclass
+class GridOrigin:
+    """
+    Represents the origin point of a 3D grid.
+
+    Attributes:
+        x (float): X-coordinate of the origin
+        y (float): Y-coordinate of the origin
+        z (float): Z-coordinate of the origin
+    """
+    x: float
+    y: float
+    z: float
+
+
+@dataclass
+class GridCellSizes:
+    """
+    Represents the cell sizes in each direction of a 3D grid.
+
+    Attributes:
+        x (List[float]): Cell sizes in the x-direction
+        y (List[float]): Cell sizes in the y-direction
+        z (List[float]): Cell sizes in the z-direction
+    """
+    x: List[float]
+    y: List[float]
+    z: List[float]
+
+
+@dataclass
+class GridData:
+    """
+    Represents a 3D grid with dimensions, origin, and cell sizes.
+
+    Attributes:
+        dimensions (GridDimensions): The dimensions of the grid
+        origin (GridOrigin): The origin point of the grid
+        cell_sizes (GridCellSizes): The cell sizes in each direction
+        metadata (Dict[str, Any]): Optional metadata about the grid
+    """
+    dimensions: GridDimensions
+    origin: GridOrigin
+    cell_sizes: GridCellSizes
+    metadata: Dict[str, Any] = field(default_factory=dict)
+
+    @classmethod
+    def from_dict(cls, grid_dict: Dict[str, Any]) -> 'GridData':
+        """
+        Converts a dictionary containing grid information into a GridData instance.
+
+        Args:
+            grid_dict: Dictionary with grid information
+
+        Returns:
+            GridData: A new GridData instance
+        """
+        dims = grid_dict["dimensions"]
+        origin_dict = grid_dict["origin"]
+        cell_sizes_dict = grid_dict["cell_sizes"]
+
+        # Handle both new and legacy key names
+        nx = dims.get("nx", dims.get("ne"))
+        ny = dims.get("ny", dims.get("nn"))
+        nz = dims.get("nz", dims.get("nz"))
+
+        x = origin_dict.get("x", origin_dict.get("x0"))
+        y = origin_dict.get("y", origin_dict.get("y0"))
+        z = origin_dict.get("z", origin_dict.get("z0"))
+
+        x_sizes = cell_sizes_dict.get("x", cell_sizes_dict.get("easting"))
+        y_sizes = cell_sizes_dict.get("y", cell_sizes_dict.get("northing"))
+        z_sizes = cell_sizes_dict.get("z", cell_sizes_dict.get("vertical"))
+
+        metadata = grid_dict.get("metadata", {})
+
+        return cls(
+            dimensions=GridDimensions(nx=nx, ny=ny, nz=nz),
+            origin=GridOrigin(x=x, y=y, z=z),
+            cell_sizes=GridCellSizes(x=x_sizes, y=y_sizes, z=z_sizes),
+            metadata=metadata
+        )
+
+
+def read_msh_structured_grid(grid_stream: TextIO, values_stream: TextIO, missing_value: Optional[float],
+                             attr_name: Optional[str]) -> StructuredData:
+    """
+    Read a structured grid mesh and values from streams and return a StructuredData object.
+
+    This function is designed to work with streams (e.g., from Azure blob storage)
+    rather than file paths.
+
+    Args:
+        grid_stream: TextIO stream containing the grid definition (.msh format)
+        values_stream: TextIO stream containing the property values (.mod format)
+
+    Returns:
+        StructuredData object containing the grid and property values
+
+    Raises:
+        ValueError: If the stream format is invalid
+    """
+    # Read all lines from the grid stream
+    lines = [line.strip() for line in grid_stream if line.strip()]
+
+    # Create metadata for the grid
+    metadata = {
+            'file_format': 'grav3d',
+            'source'     : 'stream'
+    }
+
+    # Parse grid information from lines
+    try:
+        grid = _parse_grid_from_lines(lines, metadata)
+    except ValueError as e:
+        # Add context about the stream to the error message
+        raise ValueError(f"Error parsing grid stream: {e}") from e
+
+    # Read values from the values stream
+    try:
+        # Read all values from the stream
+        lines = [line.strip() for line in values_stream if line.strip()]
+
+        model_array = _parse_mod_file(grid, lines, missing_value=missing_value)
+
+    except Exception as e:
+        # Add context to any errors
+        raise ValueError(f"Error reading model stream: {str(e)}") from e
+
+    # Create and return a StructuredData object
+    return structured_data_from(model_array, grid, data_name=attr_name)
+
+
+def read_msh_file(filepath: Union[str, Path]) -> GridData:
+    """
+    Read a structured grid mesh file and return a GridData object.
+
+    Currently supports Grav3D mesh file format (.msh):
+    - First line: NX NY NZ (number of cells in X, Y, Z directions)
+    - Second line: X Y Z (coordinates of origin in meters)
+    - Next section: X cell widths (either expanded or using N*value notation)
+    - Next section: Y cell widths (either expanded or using N*value notation)
+    - Next section: Z cell thicknesses (either expanded or using N*value notation)
+
+    Args:
+        filepath: Path to the mesh file
+
+    Returns:
+        GridData object containing the mesh information
+
+    Raises:
+        FileNotFoundError: If the file doesn't exist
+        ValueError: If the file format is invalid
+    """
+    filepath = Path(filepath)
+    if not filepath.exists():
+        raise FileNotFoundError(f"Mesh file not found: {filepath}")
+
+    with open(filepath, 'r') as f:
+        lines = [line.strip() for line in f.readlines() if line.strip()]
+
+    metadata = {
+            'file_format': 'grav3d',
+            'filepath'   : str(filepath)
+    }
+
+    try:
+        return _parse_grid_from_lines(lines, metadata)
+    except ValueError as e:
+        # Add context about the file to the error message
+        raise ValueError(f"Error parsing mesh file {filepath}: {e}") from e
+
+
+def read_mod_file(filepath: Union[str, Path], grid: GridData,
+                  missing_value: float = -99_999.0) -> np.ndarray:
+    """
+    Read a model file containing property values for a 3D grid.
+
+    Currently supports Grav3D model file format (.mod) where each line contains
+    a single property value. The values are ordered with the z-direction changing
+    fastest, then x, then y.
+
+    Args:
+        filepath: Path to the model file
+        grid: GridData object containing the grid dimensions
+        missing_value: Value to replace with NaN in the output array (default: -99_999.0)
+
+    Returns:
+        3D numpy array of property values with shape (ny, nx, nz)
+
+    Raises:
+        FileNotFoundError: If the file doesn't exist
+        ValueError: If the number of values doesn't match the grid dimensions
+    """
+    filepath = Path(filepath)
+    if not filepath.exists():
+        raise FileNotFoundError(f"Model file not found: {filepath}")
+
+    try:
+        # Read all values from the file
+        with open(filepath, 'r') as f:
+            lines = [line.strip() for line in f if line.strip()]
+
+        model_array = _parse_mod_file(grid, lines, missing_value)
+
+        return model_array
+
+    except Exception as e:
+        # Add context to any errors
+        raise ValueError(f"Error reading model file {filepath}: {str(e)}") from e
+
+
+def _parse_mod_file(grid: GridData, lines: List[str], missing_value: Optional[float]) -> np.ndarray:
+    # Convert each line to a float
+    values = np.array([float(line) for line in lines], dtype=float)
+    # Calculate expected number of values based on grid dimensions
+    nx, ny, nz = grid.dimensions.nx, grid.dimensions.ny, grid.dimensions.nz
+    expected_count = nx * ny * nz
+    if len(values) != expected_count:
+        raise ValueError(
+            f"Invalid model file: expected {expected_count} values, got {len(values)}"
+        )
+    # Reshape to (ny, nx, nz) with z changing fastest
+    model_array = values.reshape((ny, nx, nz))
+    # Replace missing values with NaN
+    if missing_value is not None:
+        model_array[model_array == missing_value] = np.nan
+    return model_array
+
+
+def structured_data_from(array: np.ndarray, grid: GridData,
+                         data_name: str = 'model') -> StructuredData:
+    """
+    Convert a 3D numpy array and grid information into a StructuredData object.
+
+    Args:
+        array: 3D numpy array of property values with shape (ny, nx, nz)
+        grid: GridData object containing grid dimensions, origin, and cell sizes
+        data_name: Name for the data array (default: 'model')
+
+    Returns:
+        StructuredData object containing the data array with proper coordinates
+
+    Raises:
+        ValueError: If array shape doesn't match grid dimensions
+    """
+    # Verify array shape matches grid dimensions
+    expected_shape = (grid.dimensions.ny, grid.dimensions.nx, grid.dimensions.nz)
+    if array.shape != expected_shape:
+        raise ValueError(
+            f"Array shape {array.shape} doesn't match grid dimensions {expected_shape}"
+        )
+
+    # Calculate cell center coordinates
+    centers = _calculate_cell_centers(grid)
+
+    # Create the xarray DataArray with proper coordinates
+    xr_data_array = xr.DataArray(
+        data=array,
+        dims=['y', 'x', 'z'],  # Dimensions in the order they appear in the array
+        coords={
+                'x': centers['x'],
+                'y': centers['y'],
+                'z': centers['z'],
+        },
+        name=data_name,
+        attrs=grid.metadata  # Include grid metadata in the data array
+    )
+
+    # Create a StructuredData instance from the xarray DataArray
+    struct = StructuredData.from_data_array(
+        data_array=xr_data_array,
+        data_array_name=data_name
+    )
+
+    return struct
+
+
+def _parse_grid_from_lines(lines: List[str], metadata: Dict[str, Any] = None) -> GridData:
+    """
+    Parse grid information from a list of lines.
+
+    Args:
+        lines: List of lines containing grid information
+        metadata: Optional metadata to include in the GridData object
+
+    Returns:
+        GridData object containing the parsed grid information
+
+    Raises:
+        ValueError: If the lines format is invalid
+    """
+    if len(lines) < 2:
+        raise ValueError("Invalid format: insufficient data")
+
+    # Parse dimensions (first line)
+    try:
+        dims = lines[0].split()
+        nx, ny, nz = int(dims[0]), int(dims[1]), int(dims[2])
+    except (IndexError, ValueError) as e:
+        raise ValueError(f"Invalid dimensions: {e}")
+
+    # Parse origin coordinates (second line)
+    try:
+        origin = lines[1].split()
+        x, y, z = float(origin[0]), float(origin[1]), float(origin[2])
+    except (IndexError, ValueError) as e:
+        raise ValueError(f"Invalid origin: {e}")
+
+    # Parse cell sizes
+    try:
+        current_line = 2
+        x_sizes, current_line = _parse_cell_sizes(lines, current_line, nx)
+        y_sizes, current_line = _parse_cell_sizes(lines, current_line, ny)
+        z_sizes, _ = _parse_cell_sizes(lines, current_line, nz)
+    except (IndexError, ValueError) as e:
+        raise ValueError(f"Error parsing cell sizes: {e}")
+
+    # Create a GridData object with the parsed information
+    grid_data_dict = {
+            'dimensions': {'nx': nx, 'ny': ny, 'nz': nz},
+            'origin'    : {'x': x, 'y': y, 'z': z},
+            'cell_sizes': {
+                    'x': x_sizes,
+                    'y': y_sizes,
+                    'z': z_sizes
+            },
+            'metadata'  : metadata or {}
+    }
+
+    return GridData.from_dict(grid_data_dict)
+
+
+def _parse_cell_sizes(lines: List[str], start_index: int, count: int) -> Tuple[List[float], int]:
+    """
+    Parse cell sizes from file lines, handling both compact (N*value) and expanded notation.
+
+    Args:
+        lines: List of lines from the file
+        start_index: Index to start parsing from
+        count: Number of values to parse
+
+    Returns:
+        Tuple containing:
+            - List of parsed values
+            - Next line index after parsing
+    """
+    line = lines[start_index]
+
+    # Check for compact notation (N*value)
+    if '*' in line:
+        parts = line.split('*')
+        repetition = int(parts[0])
+        value = float(parts[1])
+        values = [value] * repetition
+        return values, start_index + 1
+
+    # Handle expanded notation across multiple lines
+    values = []
+    line_index = start_index
+
+    while len(values) < count and line_index < len(lines):
+        current_line = lines[line_index]
+
+        # If we encounter a line with compact notation while parsing expanded, 
+        # it's likely the next section
+        if '*' in current_line and len(values) > 0:
+            break
+
+        # Add all numbers from the current line
+        values.extend([float(x) for x in current_line.split()])
+        line_index += 1
+
+    # Take only the required number of values
+    return values[:count], line_index
+
+
+def _calculate_cell_centers(grid: GridData) -> Dict[str, np.ndarray]:
+    """
+    Calculate the center coordinates of each cell in the grid.
+
+    Args:
+        grid: GridData object containing grid dimensions, origin, and cell sizes
+
+    Returns:
+        Dictionary with 'x', 'y', and 'z' keys containing arrays of cell center coordinates
+    """
+    # Convert cell sizes to numpy arrays for vectorized operations
+    x_sizes = np.array(grid.cell_sizes.x)
+    y_sizes = np.array(grid.cell_sizes.y)
+    z_sizes = np.array(grid.cell_sizes.z)
+
+    # Calculate cell centers by adding cumulative sizes and offsetting by half the first cell size
+    x_centers = grid.origin.x + np.cumsum(x_sizes) - x_sizes[0] / 2
+    y_centers = grid.origin.y + np.cumsum(y_sizes) - y_sizes[0] / 2
+
+    # For z, cells typically extend downward from the origin
+    z_centers = grid.origin.z - (np.cumsum(z_sizes) - z_sizes[0] / 2)
+
+    return {
+            'x': x_centers,
+            'y': y_centers,
+            'z': z_centers
+    }

{subsurface_terra-2025.1.0rc11 → subsurface_terra-2025.1.0rc13/subsurface_terra.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: subsurface_terra
-Version: 2025.1.0rc11
+Version: 2025.1.0rc13
 Summary: Subsurface data types and utilities. This version is the one used by Terranigma Solutions. Please feel free to take anything in this repository for the original one.
 Home-page: https://softwareunderground.github.io/subsurface
 Author: Software Underground

{subsurface_terra-2025.1.0rc11 → subsurface_terra-2025.1.0rc13}/subsurface_terra.egg-info/SOURCES.txt

@@ -85,6 +85,7 @@ subsurface/modules/reader/profiles/profiles_core.py
 subsurface/modules/reader/topography/__init__.py
 subsurface/modules/reader/topography/topo_core.py
 subsurface/modules/reader/volume/__init__.py
+subsurface/modules/reader/volume/read_grav3d.py
 subsurface/modules/reader/volume/read_volume.py
 subsurface/modules/reader/volume/segy_reader.py
 subsurface/modules/reader/volume/seismic.py