subsurface-terra 2025.1.0rc8__py3-none-any.whl → 2025.1.0rc11__py3-none-any.whl

subsurface/_version.py

@@ -17,5 +17,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '2025.1.0rc8'
+__version__ = version = '2025.1.0rc11'
 __version_tuple__ = version_tuple = (2025, 1, 0)

subsurface/core/geological_formats/boreholes/survey.py

@@ -111,9 +111,11 @@ def _map_attrs_to_measured_depths(attrs: pd.DataFrame, survey: Survey) -> pd.Dat
 
     # Start with a copy of the existing attributes DataFrame
     new_attrs = survey.survey_trajectory.data.points_attributes.copy()
-    if 'component lith' in attrs.columns:
+    if 'component lith' in attrs.columns and 'lith_ids' not in attrs.columns:
         # Factorize lith components directly in-place
         attrs['lith_ids'], _ = pd.factorize(attrs['component lith'], use_na_sentinel=True)
+    else:
+        pass
 
     # Add missing columns from attrs, preserving their dtypes
     for col in attrs.columns.difference(new_attrs.columns):
@@ -152,7 +154,7 @@ def _map_attrs_to_measured_depths(attrs: pd.DataFrame, survey: Survey) -> pd.Dat
                 continue
             attr_to_interpolate = attrs_well[col]
             # make sure the attr_to_interpolate is not a string
-            if attr_to_interpolate.dtype == 'O':
+            if attr_to_interpolate.dtype == 'O' or isinstance(attr_to_interpolate.dtype, pd.CategoricalDtype): 
                 continue
             if col in ['lith_ids', 'component lith']:
                 interp_kind = 'nearest'

subsurface/modules/reader/mesh/_trimesh_reader.py

@@ -37,9 +37,9 @@ def load_with_trimesh(path_to_file_or_buffer, file_type: Optional[str] = None,
             # Old Z axis → New -Y axis
             # Old X axis → Remains as X axis
             transform = np.array([
-                    [1, 0, 0, 0],  # X → X
-                    [0, 0, 1, 0],  # Y → Z 
-                    [0, 1, 0, 0],  # Z → -Y
+                    [1, 0, 0, 0],  
+                    [0, 0, -1, 0],  
+                    [0, 1, 0, 0], 
                     [0, 0, 0, 1]
             ])
 

subsurface/modules/reader/mesh/mx_reader.py

@@ -157,7 +157,7 @@ def _process_mesh(mesh_lines) -> Optional[GOCADMesh]:
             continue
 
         if in_tface:
-            if line.startswith('VRTX'):
+            if line.startswith('VRTX') or line.startswith('PVRTX'):
                 # Parse vertex line
                 parts = line.split()
                 if len(parts) >= 5:
@@ -167,6 +167,7 @@ def _process_mesh(mesh_lines) -> Optional[GOCADMesh]:
                     vertex_indices.append(vid)
                     vertex_list.append([x, y, z])
                     vid_to_index[vid] = len(vertex_list) - 1
+                    # If PVRTX then there could be more columns with property values. For now, we are just parsing the vertex coordinates.
                 continue
             elif line.startswith('ATOM'):
                 # Parse ATOM line

subsurface/modules/reader/volume/read_volume.py

@@ -7,6 +7,7 @@ from subsurface.core.structs import StructuredData
 from .... import optional_requirements
 from ....core.structs import UnstructuredData
 from subsurface.core.reader_helpers.readers_data import GenericReaderFilesHelper
+import numpy as np
 import pandas as pd
 
 
@@ -32,7 +33,7 @@ def read_VTK_structured_grid(file_or_buffer: Union[str, BytesIO], active_scalars
         # If it's a file path, read directly
         pyvista_obj = pv.read(file_or_buffer)
     try:
-        pyvista_struct: pv.ExplicitStructuredGrid = pyvista_obj.cast_to_explicit_structured_grid()
+        pyvista_struct: pv.ExplicitStructuredGrid = pv_cast_to_explicit_structured_grid(pyvista_obj)
     except Exception as e:
         raise f"The file is not a structured grid: {e}"
 
@@ -99,3 +100,131 @@ def read_volumetric_mesh_attr_file(reader_helper: GenericReaderFilesHelper) -> p
     df = pd.read_table(reader_helper.file_or_buffer, **reader_helper.pandas_reader_kwargs)
     df.columns = df.columns.astype(str).str.strip()
     return df
+
+
+def pv_cast_to_explicit_structured_grid(pyvista_object: 'pv.DataSet') -> 'pv.ExplicitStructuredGrid':
+    pv = optional_requirements.require_pyvista()
+
+    match pyvista_object:
+        case pv.RectilinearGrid() as rectl_grid:
+            return __pv_convert_rectilinear_to_explicit(rectl_grid)
+        case pv.UnstructuredGrid() as unstr_grid:
+            return __pv_convert_unstructured_to_explicit(unstr_grid)
+        case _:
+            return pyvista_object.cast_to_explicit_structured_grid()
+
+
+def __pv_convert_unstructured_to_explicit(unstr_grid):
+    """
+    Convert a PyVista UnstructuredGrid to an ExplicitStructuredGrid if possible.
+    """
+    pv = optional_requirements.require_pyvista()
+
+    # First check if the grid has the necessary attributes to be treated as structured
+    if not hasattr(unstr_grid, 'n_cells') or unstr_grid.n_cells == 0:
+        raise ValueError("The unstructured grid has no cells.")
+    
+    # Try to detect if the grid has a structured topology
+    # Check if the grid has cell type 11 (VTK_VOXEL) or 12 (VTK_HEXAHEDRON)
+    cell_types = unstr_grid.celltypes
+    
+    # Voxels (11) and hexahedra (12) are the cell types used in structured grids
+    if not all(ct in [11, 12] for ct in cell_types):
+        raise ValueError("The unstructured grid contains non-hexahedral cells and cannot be converted to explicit structured.")
+    
+    # Try to infer dimensions from the grid
+    try:
+        # Method 1: Try PyVista's built-in conversion if available
+        return unstr_grid.cast_to_explicit_structured_grid()
+    except (AttributeError, TypeError):
+        pass
+    
+    try:
+        # Method 2: If the grid has dimensions stored as field data
+        if "dimensions" in unstr_grid.field_data:
+            dims = unstr_grid.field_data["dimensions"]
+            if len(dims) == 3:
+                nx, ny, nz = dims
+                # Verify that dimensions match the number of cells
+                if (nx-1)*(ny-1)*(nz-1) != unstr_grid.n_cells:
+                    raise ValueError("Stored dimensions do not match the number of cells.")
+                
+                # Extract points and reorder if needed
+                points = unstr_grid.points.reshape((nx, ny, nz, 3))
+                
+                # Create explicit structured grid
+                explicit_grid = pv.ExplicitStructuredGrid((nx, ny, nz), points.reshape((-1, 3)))
+                explicit_grid.compute_connectivity()
+                
+                # Transfer data arrays
+                for name, array in unstr_grid.cell_data.items():
+                    explicit_grid.cell_data[name] = array.copy()
+                for name, array in unstr_grid.point_data.items():
+                    explicit_grid.point_data[name] = array.copy()
+                for name, array in unstr_grid.field_data.items():
+                    if name != "dimensions":  # Skip dimensions field
+                        explicit_grid.field_data[name] = array.copy()
+                
+                return explicit_grid
+    except (ValueError, KeyError):
+        pass
+    
+    # If none of the above methods work, use PyVista's extract_cells function
+    # to reconstruct the structured grid if possible
+    try:
+        # This is a best-effort approach that tries multiple strategies
+        return pv.core.filters.convert_unstructured_to_structured_grid(unstr_grid)
+    except Exception as e:
+        raise ValueError(f"Failed to convert unstructured grid to explicit structured grid: {e}")
+    
+def __pv_convert_rectilinear_to_explicit(rectl_grid):
+
+    pv = optional_requirements.require_pyvista()
+
+    # Extract the coordinate arrays from the input RectilinearGrid.
+    x = np.asarray(rectl_grid.x)
+    y = np.asarray(rectl_grid.y)
+    z = np.asarray(rectl_grid.z)
+
+    # Helper function: "double" the coordinates to produce an expanded set
+    # that, when processed internally via np.unique, returns the original nodal values.
+    def doubled_coords(arr):
+        return np.repeat(arr, 2)[1:-1]
+
+    # Double the coordinate arrays.
+    xcorn = doubled_coords(x)
+    ycorn = doubled_coords(y)
+    zcorn = doubled_coords(z)
+
+    # Build a complete grid of corner points via meshgrid. Fortran ('F') order ensures
+    # the connectivity ordering aligns with VTK's expectations.
+    xx, yy, zz = np.meshgrid(xcorn, ycorn, zcorn, indexing='ij')
+    corners = np.column_stack((xx.ravel(order='F'),
+                               yy.ravel(order='F'),
+                               zz.ravel(order='F')))
+
+    # The dimensions to pass to the ExplicitStructuredGrid constructor should be
+    # the counts of unique coordinates in each direction.
+    dims = (len(np.unique(xcorn)),
+            len(np.unique(ycorn)),
+            len(np.unique(zcorn)))
+
+    # Create the ExplicitStructuredGrid.
+    explicit_grid = pv.ExplicitStructuredGrid(dims, corners)
+    explicit_grid.compute_connectivity()
+
+    # --- Copy associated data arrays ---
+
+    # Transfer all cell data arrays.
+    for name, array in rectl_grid.cell_data.items():
+        explicit_grid.cell_data[name] = array.copy()
+
+    # Transfer all point data arrays.
+    for name, array in rectl_grid.point_data.items():
+        explicit_grid.point_data[name] = array.copy()
+
+    # (Optional) Transfer field data as well.
+    for name, array in rectl_grid.field_data.items():
+        explicit_grid.field_data[name] = array.copy()
+
+    return explicit_grid

subsurface/modules/reader/wells/read_borehole_interface.py

@@ -100,6 +100,16 @@ def _validate_lith_data(d: pd.DataFrame, reader_helper: GenericReaderFilesHelper
         raise AttributeError('If wells attributes represent lithology, `component lith` column must be present in the file. '
                              'Use columns_map to assign column names to these fields. Maybe you are marking as lithology'
                              'the wrong file?')
+    else:
+        # TODO: Add categories to reader helper
+        categories = sorted(d['component lith'].dropna().unique())
+        d['component lith'] = pd.Categorical(
+            d['component lith'],
+            categories=categories,
+            ordered=True
+        )
+        
+        d['lith_ids'] = d['component lith'].cat.codes + 1
 
     given_top = np.isin(['top', 'base'], d.columns).all()
     given_altitude_and_base = np.isin(['altitude', 'base'], d.columns).all()

subsurface/modules/tools/mocking_aux.py

@@ -0,0 +1,104 @@
+import numpy as np
+import pyvista as pv
+
+
+def transform_gaussian_blur(grid, sigma=20.0):
+    """
+    Applies a Gaussian blur to the 'model_name' field of the structured grid.
+
+    Parameters:
+        grid - PyVista grid with 'model_name' field
+        sigma - Standard deviation for the Gaussian kernel
+    """
+    from scipy.ndimage import gaussian_filter
+
+    # Get the original dimensions of the grid
+    dims = grid.dimensions
+
+    # Reshape the data to 3D array matching grid dimensions
+    values = np.array(grid['model_name'])
+    values_3d = values.reshape(dims[2] - 1, dims[1] - 1, dims[0] - 1).transpose(2, 1, 0)
+
+    # Apply Gaussian filter
+    blurred_values = gaussian_filter(values_3d, sigma=sigma, axes=(2,))
+
+    # Reshape back to 1D array
+    grid['model_name'] = blurred_values.transpose(2, 1, 0).flatten()
+    return grid
+
+
+def transform_sinusoidal(values, amplitude=1.0, frequency=0.01, phase=0):
+    """
+    Apply a sinusoidal transformation to the values.
+    """
+    return values + amplitude * np.sin(frequency * values + phase)
+
+
+def obfuscate_model_name(grid, transform_functions, attr):
+    """
+    Applies transformation functions to the 'model_name' field.
+    Functions can operate on either the grid or the values array.
+    """
+    for func in transform_functions:
+        if 'grid' in func.__code__.co_varnames:
+            # Function expects the full grid
+            grid = func(grid)
+        else:
+            # Function expects just the values array
+            values = np.array(grid[attr])
+            grid[attr] = func(values)
+
+    return grid
+
+
+# pyvista_struct = transform_xy_to_z_propagation(pyvista_struct, z_factor=0.3, noise_level=0.1)
+def transform_subtract_mean(values):
+    """
+    Subtract the mean of the array from each element.
+    """
+    return values - np.mean(values)
+
+
+def transform_scale(values, scale_factor=0.003):
+    """
+    Multiply each value by scale_factor.
+    """
+    return values * scale_factor
+
+
+
+
+def update_extent(pyvista_grid, new_extent):
+    # new_extent: array-like with 6 elements [xmin, xmax, ymin, ymax, zmin, zmax]
+    old_bounds = np.array(pyvista_grid.bounds)  # [xmin, xmax, ymin, ymax, zmin, zmax]
+
+    # Check for valid extents
+    if any(new_extent[i] >= new_extent[i + 1] for i in range(0, 6, 2)):
+        raise ValueError("Each min value must be less than the corresponding max value in the new extent.")
+
+    # Compute old ranges and new ranges for each axis
+    old_ranges = old_bounds[1::2] - old_bounds[0::2]  # [x_range, y_range, z_range]
+    new_ranges = np.array([new_extent[1] - new_extent[0],
+                           new_extent[3] - new_extent[2],
+                           new_extent[5] - new_extent[4]])
+
+    # Avoid division by zero if any old range is zero
+    if np.any(old_ranges == 0):
+        raise ValueError("One of the dimensions in the current grid has zero length.")
+
+    # Get the old points and reshape for easier manipulation
+    old_points = pyvista_grid.points  # shape (N, 3)
+
+    # Compute normalized coordinates within the old extent
+    norm_points = (old_points - old_bounds[0::2]) / old_ranges
+
+    # Compute new points based on new extent
+    new_mins = np.array([new_extent[0], new_extent[2], new_extent[4]])
+    new_points = new_mins + norm_points * new_ranges
+
+    # Update the grid's points
+    pyvista_grid.points = new_points
+
+    # Updating bounds is implicit once the points are modified.
+    pyvista_grid.Modified()
+    return pyvista_grid

{subsurface_terra-2025.1.0rc8.dist-info → subsurface_terra-2025.1.0rc11.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: subsurface_terra
-Version: 2025.1.0rc8
+Version: 2025.1.0rc11
 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-2025.1.0rc8.dist-info → subsurface_terra-2025.1.0rc11.dist-info}/RECORD

@@ -1,5 +1,5 @@
 subsurface/__init__.py,sha256=0D2rCUem3fiHsXFXXSmwheLiPS4cXxEdfWdFBj0b-cY,930
-subsurface/_version.py,sha256=0-BBA5HgwLud0-RzWFjmovo55cqFKf4y2LQ_O3YdbRs,541
+subsurface/_version.py,sha256=k9Z1PFW4N27hJOHdtsBGeU2nnn-S8fhplPVjgvRiS9Q,542
 subsurface/optional_requirements.py,sha256=Wg36RqxzPiLtN-3qSg5K9QVEeXCB0-EjSzHERAoO8EE,2883
 subsurface/api/__init__.py,sha256=UiOBKQcZJGMeh_5ZNhXqT2iEdiIk721djLX30aFxEa4,341
 subsurface/api/interfaces/__init__.py,sha256=rqUtJyMLicobcyhmr74TepjmUQAEmlazKT3vjV_n3aA,6
@@ -13,7 +13,7 @@ subsurface/core/geological_formats/boreholes/__init__.py,sha256=47DEQpj8HBSa-_TI
 subsurface/core/geological_formats/boreholes/_combine_trajectories.py,sha256=U5VribebcMAag0DOKnna983g1BXAGLKCddGra2g3Nos,5246
 subsurface/core/geological_formats/boreholes/boreholes.py,sha256=Q7KBYIk9M4-SZjDOVx5dMp8DnHBo4VTFrJ4jAKCmrJ8,5256
 subsurface/core/geological_formats/boreholes/collars.py,sha256=o1I8bS0XqWa2fS0n6XZVKXsuBHknXO2Z_5sdlFc_GAE,750
-subsurface/core/geological_formats/boreholes/survey.py,sha256=6UJRFCp-WAEgTB1YboTGrSyrtKhJNCm1R31jjssqrkA,16095
+subsurface/core/geological_formats/boreholes/survey.py,sha256=aaENR0ksT_lK0BYR7HL73KNZ44eo3Ag353xQdVcLOz0,16219
 subsurface/core/reader_helpers/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 subsurface/core/reader_helpers/reader_unstruct.py,sha256=Lme1ano-dQrKhLCwrokcpKqa28DFxDaGAs3ub8MAHtY,397
 subsurface/core/reader_helpers/readers_data.py,sha256=Vewi8pqv-zooRIhffTM52eWZeP6l9MnHkD9LZj6c1LU,4995
@@ -45,11 +45,11 @@ subsurface/modules/reader/faults/faults.py,sha256=s144Gq0tFvjSUkB66dB86kYjW2l2e1
 subsurface/modules/reader/geo_object/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 subsurface/modules/reader/mesh/_GOCAD_mesh.py,sha256=_MwNy4iVMGnemvT01hhB-nbCc8a1r8ETEAkD-AWcBz4,3304
 subsurface/modules/reader/mesh/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-subsurface/modules/reader/mesh/_trimesh_reader.py,sha256=-cmm-BYIUC9x6tqABNgKzNMSrDfuoTdZ7YpfB1nNPh0,17260
+subsurface/modules/reader/mesh/_trimesh_reader.py,sha256=GPKFwWbWuvL-RvY_cGjEaRghBUda2mIxY4mbEp0AVEk,17231
 subsurface/modules/reader/mesh/csv_mesh_reader.py,sha256=0iXYg-JOLUg7yH6Rw6qCoxXvKh0hOUTwjYxbhSlGfGM,1969
 subsurface/modules/reader/mesh/dxf_reader.py,sha256=JDhzFRE46sdwMGBB8enHNluH07ohqt6LhgLHiSQRL-I,6525
 subsurface/modules/reader/mesh/glb_reader.py,sha256=dierR9AYM5Q2szLuemfLlM_JcPRNtDrD5fpF8zNjBS8,1118
-subsurface/modules/reader/mesh/mx_reader.py,sha256=o1OPnGSSOjJCpLCzazRsmjhFxhbYrCi6zTTRnKtCJ30,8419
+subsurface/modules/reader/mesh/mx_reader.py,sha256=YQqvOJ4FuPrlz_3bHIdqT-9YKkirF_Vbjnv6cVQnwAw,8587
 subsurface/modules/reader/mesh/obj_reader.py,sha256=LXf-N-So5xWhnZ6uHJPjcCfQM71a_mqJa3hQEikOGzU,2207
 subsurface/modules/reader/mesh/omf_mesh_reader.py,sha256=0gewosxlLVTQQoUyvYB91AOZ_SByQqxw53coSwCKeMI,1436
 subsurface/modules/reader/mesh/surface_reader.py,sha256=EcRjr3sAJbwZpqm7WHHe1bnMZyGO5MSgF6qm5bSBLtQ,2420
@@ -60,19 +60,21 @@ subsurface/modules/reader/profiles/profiles_core.py,sha256=kqlt79hjdWWQNBjWqLGlu
 subsurface/modules/reader/topography/__init__.py,sha256=zkaTX5JxsNfjF-dFeEbHfUB58vhPMjm6Iiqx9HgJOrY,14
 subsurface/modules/reader/topography/topo_core.py,sha256=6rkDp9XrUSif8ZuraDrUK2I8-yqEp8CRm4r4l2lQuw0,3542
 subsurface/modules/reader/volume/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-subsurface/modules/reader/volume/read_volume.py,sha256=Dlv7G5GYikdZCp9H5SMfL9vSsUAKpc4b3vBB-P7IVBM,4025
+subsurface/modules/reader/volume/read_volume.py,sha256=GvlYIROefskHkqpwvSu60jQIzev54jBfbrL74CYT7TU,9580
 subsurface/modules/reader/volume/segy_reader.py,sha256=oBS1FwwzFTMBmAR3odJMvW-as_0YMudPcFmndpcApW4,3958
 subsurface/modules/reader/volume/seismic.py,sha256=dRA7YKw9fkrkAYS7Bnfm7GfCPdfxVsDyfM7frQK56V4,4950
 subsurface/modules/reader/volume/volume_utils.py,sha256=7ToIdVwq04lMyYGJE9PzYVQt9xl9mjbXXrzvMfM6wGw,1367
 subsurface/modules/reader/wells/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 subsurface/modules/reader/wells/_read_to_df.py,sha256=PFs5ottnm7LtzmJgPh8UN3cdR4j2y734RTDPoks16ls,2294
-subsurface/modules/reader/wells/read_borehole_interface.py,sha256=iyoaee00vfSzqF4sWy9WA4a92VtEb16ERbrkdWgWszE,5548
+subsurface/modules/reader/wells/read_borehole_interface.py,sha256=1Kq_IjHhhPgxQKjk5B655CT9wCYCYz5T4UjggF8Pdfg,5899
 subsurface/modules/reader/wells/wells_utils.py,sha256=CoVF9Qtba8Qu42JcVmtsyaSS_PA80lcJ6mzh6-TQt2Q,2206
 subsurface/modules/reader/wells/DEP/__init__.py,sha256=8PES2m_HqZtZ-jFhPynJWpk8dovKAh1UyVnfAxg_NXY,1887
 subsurface/modules/reader/wells/DEP/_well_files_reader.py,sha256=QYZ9p7iyGt1JDlkrFpYPFaMnXwLj7wdFZmTYiO2niSY,6216
 subsurface/modules/reader/wells/DEP/_wells_api.py,sha256=SZU0cwfbn-bqKaAIG94be9Azxyx0pnvZrE2yXxIIJD4,2334
 subsurface/modules/reader/wells/DEP/_welly_reader.py,sha256=ktBEswaQSj0mzubFME8oTP7sTPDI1r65zVfT91LORMI,6468
 subsurface/modules/reader/wells/DEP/pandas_to_welly.py,sha256=Z67LE6K4Dy5LkR6ZrAmQx9u0UbLJj8oWxAALVx_eyDc,6925
+subsurface/modules/tools/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+subsurface/modules/tools/mocking_aux.py,sha256=DcavlyWV5pFl31MHUgOxAXW2I_y8bKqbyesBfCDWnLs,3581
 subsurface/modules/visualization/__init__.py,sha256=Y9SUj2cflk0ulCj1F1cJAeoCQJOD0eN4E98wxZ5Zhj0,65
 subsurface/modules/visualization/to_pyvista.py,sha256=_xM4Xx3PD0wyxtUrMHS5k6xbiDQ5k_Kis8dE-wnM77M,10514
 subsurface/modules/writer/__init__.py,sha256=1oDGj2X1G-R2ZRi_8sMBfq1QHkUarbycmMVvSdSTk-g,50
@@ -86,8 +88,8 @@ subsurface/modules/writer/to_rex/material_encoder.py,sha256=zGlqF9X_Civ9VvtGwo-I
 subsurface/modules/writer/to_rex/mesh_encoder.py,sha256=6TBtJhYJEAMEBHxQkbweXrJO1jIUx1ClM8l5ajVCrLc,6443
 subsurface/modules/writer/to_rex/to_rex.py,sha256=njsm2d3e69pRVfF_TOC_hexvXPmgNTZdJvhbnXcvyIo,3800
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