subsurface-terra 2025.1.0rc16__py3-none-any.whl → 2025.1.0rc17__py3-none-any.whl

subsurface/_version.py

@@ -28,7 +28,7 @@ version_tuple: VERSION_TUPLE
 commit_id: COMMIT_ID
 __commit_id__: COMMIT_ID
 
-__version__ = version = '2025.1.0rc16'
-__version_tuple__ = version_tuple = (2025, 1, 0, 'rc16')
+__version__ = version = '2025.1.0rc17'
+__version_tuple__ = version_tuple = (2025, 1, 0, 'rc17')
 
 __commit_id__ = commit_id = None

subsurface/core/structs/base_structures/_aux.py

@@ -0,0 +1,69 @@
+import pandas as pd
+
+
+def safe_convert_to_float32(df: pd.DataFrame, error_handling: str = 'raise') -> pd.DataFrame:
+    """
+    Convert DataFrame columns to float32, handling non-convertible columns.
+
+    Args:
+        df: DataFrame to convert
+        error_handling: How to handle non-convertible columns:
+            - 'raise': Raise an error
+            - 'skip': Skip non-convertible columns
+            - 'drop': Drop non-convertible columns
+
+    Returns:
+        DataFrame with converted columns
+    """
+    convertible, non_convertible = _check_convertible_to_float32(df)
+
+    if non_convertible:
+        if error_handling == 'raise':
+            raise ValueError(
+                f"Cannot convert columns to float32: {non_convertible}. "
+                f"These columns contain non-numeric data."
+            )
+        elif error_handling == 'skip':
+            # Only convert the convertible columns
+            result = df.copy()
+            for col in convertible:
+                result[col] = df[col].astype('float32')
+            return result
+        elif error_handling == 'drop':
+            # Drop non-convertible columns
+            return df[convertible].astype('float32')
+        else:
+            raise ValueError(f"Invalid error_handling: {error_handling}")
+
+    return df.astype('float32')
+
+
+def _check_convertible_to_float32(df: pd.DataFrame) -> tuple[list[str], list[str]]:
+    """
+    Check which columns in a DataFrame can be safely converted to float32.
+
+    Returns:
+        tuple: (convertible_columns, non_convertible_columns)
+    """
+    convertible = []
+    non_convertible = []
+
+    for col in df.columns:
+        if pd.api.types.is_numeric_dtype(df[col]):
+            # Already numeric, can convert
+            convertible.append(col)
+        elif pd.api.types.is_bool_dtype(df[col]):
+            # Boolean can be converted (True->1.0, False->0.0)
+            convertible.append(col)
+        elif pd.api.types.is_string_dtype(df[col]) or pd.api.types.is_object_dtype(df[col]):
+            # Try to convert to numeric
+            try:
+                pd.to_numeric(df[col], errors='raise')
+                convertible.append(col)
+            except (ValueError, TypeError):
+                non_convertible.append(col)
+        else:
+            # Other types (datetime, timedelta, categorical, etc.)
+            non_convertible.append(col)
+
+    return convertible, non_convertible

subsurface/core/structs/base_structures/unstructured_data.py

@@ -299,6 +299,25 @@ class UnstructuredData:
         bytearray_le = vertex + cells + cell_attribute + vertex_attribute
         return bytearray_le
 
+    def _to_bytearray(self, order):
+        from subsurface.core.structs.base_structures._aux import safe_convert_to_float32
+        vertex = self.vertex.astype('float32').tobytes(order)
+        cells = self.cells.astype('int32').tobytes(order)
+
+        # Only include numeric columns
+        cell_attribute = safe_convert_to_float32(
+            self.attributes,
+            error_handling='drop'
+        ).values.tobytes(order)
+
+        vertex_attribute = safe_convert_to_float32(
+            self.points_attributes,
+            error_handling='drop'
+        ).values.tobytes(order)
+
+        bytearray_le = vertex + cells + cell_attribute + vertex_attribute
+        return bytearray_le
+
     def _validate(self):
         try:
             _ = self.data[self.cells_attr_name]['cell']

subsurface/modules/reader/volume/read_grav3d.py

@@ -106,10 +106,9 @@ class GridData:
         )
 
 
-from typing import Literal
 
 def read_msh_structured_grid(grid_stream: TextIO, values_stream: TextIO, missing_value: Optional[float],
-                             attr_name: Optional[str], ordering: Literal['ijk', 'xyz', 'xyz_reverse'] = 'ijk') -> StructuredData:
+                             attr_name: Optional[str]) -> StructuredData:
     """
     Read a structured grid mesh and values from streams and return a StructuredData object.
 
@@ -121,12 +120,7 @@ def read_msh_structured_grid(grid_stream: TextIO, values_stream: TextIO, missing
         values_stream: TextIO stream containing the property values (.mod format)
         missing_value: Value to replace with NaN in the output array
         attr_name: Name for the data attribute
-        ordering: Data ordering in the file:
-                  - 'ijk': i (x) varies fastest, then j (y), then k (z)
-                  - 'xyz': z varies fastest, then x, then y
-                  - 'xyz_reverse': z varies fastest (reversed), then x, then y
-                  Default is 'ijk'.
-
+        
     Returns:
         StructuredData object containing the grid and property values
 
@@ -154,7 +148,7 @@ def read_msh_structured_grid(grid_stream: TextIO, values_stream: TextIO, missing
         # 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, ordering=ordering)
+        model_array = _parse_mod_file(grid, lines, missing_value=missing_value)
 
     except Exception as e:
         # Add context to any errors
@@ -206,7 +200,7 @@ def read_msh_file(filepath: Union[str, Path]) -> GridData:
 
 def read_mod_file(filepath: Union[str, Path], grid: GridData,
                   missing_value: float = -99_999.0,
-                  ordering: Literal['ijk', 'xyz', 'xyz_reverse'] = 'ijk') -> np.ndarray:
+                  ) -> np.ndarray:
     """
     Read a model file containing property values for a 3D grid.
 
@@ -217,11 +211,6 @@ def read_mod_file(filepath: Union[str, Path], grid: GridData,
         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)
-        ordering: Data ordering in the file. Options:
-                  - 'ijk': i (x) varies fastest, then j (y), then k (z) - standard VTK/Fortran ordering
-                  - 'xyz': z varies fastest, then x, then y - legacy Grav3D ordering
-                  - 'xyz_reverse': z varies fastest (reversed direction), then x, then y
-                  Default is 'ijk'.
 
     Returns:
         3D numpy array of property values with shape (ny, nx, nz)
@@ -239,7 +228,7 @@ def read_mod_file(filepath: Union[str, Path], grid: GridData,
         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, ordering)
+        model_array = _parse_mod_file(grid, lines, missing_value)
 
         return model_array
 
@@ -265,7 +254,7 @@ def structured_data_from(array: np.ndarray, grid: GridData,
         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)
+    expected_shape = (grid.dimensions.nx, grid.dimensions.ny, grid.dimensions.nz)
     if array.shape != expected_shape:
         raise ValueError(
             f"Array shape {array.shape} doesn't match grid dimensions {expected_shape}"
@@ -277,7 +266,7 @@ def structured_data_from(array: np.ndarray, grid: GridData,
     # 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
+        dims=['x', 'y', 'z'],  # Dimensions in the order they appear in the array
         coords={
                 'x': centers['x'],
                 'y': centers['y'],
@@ -424,8 +413,7 @@ def _calculate_cell_centers(grid: GridData) -> Dict[str, np.ndarray]:
     }
 
 
-def _parse_mod_file(grid: GridData, lines: List[str], missing_value: Optional[float],
-                   ordering: Literal['ijk', 'xyz', 'xyz_reverse'] = 'ijk') -> np.ndarray:
+def _parse_mod_file(grid: GridData, lines: List[str], missing_value: Optional[float]) -> np.ndarray:
     """
     Parse model file values into a 3D numpy array.
 
@@ -433,13 +421,9 @@ def _parse_mod_file(grid: GridData, lines: List[str], missing_value: Optional[fl
         grid: GridData object containing grid dimensions
         lines: List of lines containing the values
         missing_value: Value to replace with NaN
-        ordering: Data ordering in the file:
-                  - 'ijk': i (x) varies fastest, then j (y), then k (z)
-                  - 'xyz': z varies fastest, then x, then y
-                  - 'xyz_reverse': z varies fastest (reversed), then x, then y
 
     Returns:
-        3D numpy array with shape (ny, nx, nz)
+        3D numpy array with shape (nx, ny, nz)
     """
     # Convert each line to a float
     values = np.array([float(line) for line in lines], dtype=float)
@@ -453,23 +437,8 @@ def _parse_mod_file(grid: GridData, lines: List[str], missing_value: Optional[fl
             f"Invalid model file: expected {expected_count} values, got {len(values)}"
         )
     
-    # Reshape based on ordering
-    if ordering == 'ijk':
-        # i (x) varies fastest, then j (y), then k (z)
-        # This is standard VTK/Fortran ordering: (k, j, i) in array dimensions
-        model_array = values.reshape((nz, ny, nx), order='C')
-        # Transpose to (ny, nx, nz) to match expected output shape
-        model_array = np.transpose(model_array, (1, 2, 0))
-    elif ordering == 'xyz':
-        # z varies fastest, then x, then y (legacy Grav3D ordering)
-        model_array = values.reshape((ny, nx, nz))
-    elif ordering == 'xyz_reverse':
-        # z varies fastest (but in reverse direction), then x, then y
-        model_array = values.reshape((ny, nx, nz))
-        # Reverse the z-axis (last dimension)
-        model_array = np.flip(model_array, axis=2)
-    else:
-        raise ValueError(f"Invalid ordering: {ordering}. Must be 'ijk', 'xyz', or 'xyz_reverse'")
+    model_array = values.reshape((nz, nx, ny), order='F')
+    model_array = np.transpose(model_array, (1, 2, 0))[:, :, ::-1]
     
     # Replace missing values with NaN
     if missing_value is not None:

{subsurface_terra-2025.1.0rc16.dist-info → subsurface_terra-2025.1.0rc17.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: subsurface_terra
-Version: 2025.1.0rc16
+Version: 2025.1.0rc17
 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-2025.1.0rc16.dist-info → subsurface_terra-2025.1.0rc17.dist-info}/RECORD

@@ -1,5 +1,5 @@
 subsurface/__init__.py,sha256=7_KttQl8rZeJG2AIZUEA_oXRWZYkJ6DUqKjqlLgF9cA,899
-subsurface/_version.py,sha256=nb8P61QwldK25wR1CNZGY__gFCsYePG-ZOEu5h5BQFg,722
+subsurface/_version.py,sha256=gsxkMYFwv9EtAE0vhlbi1rqKVeK7ATfhxTYuf25JQK8,722
 subsurface/optional_requirements.py,sha256=SLaMSoiGTx8ea8rpHee4Zs4te0BXcxxDWC4SF0g0RuE,2767
 subsurface/api/__init__.py,sha256=Lfx7Dq0GzQsea19w8YO4v1ZSmgeLRgR6IvjvDDjjpDY,356
 subsurface/api/interfaces/__init__.py,sha256=ajz1GSNU9xYVrFEDSz6Xwg7amWQ_yvW75tQa1ZvRIWc,3
@@ -22,11 +22,12 @@ subsurface/core/reader_helpers/readers_data.py,sha256=3NEB4A48mBBUx9XM5NRZeavCn5
 subsurface/core/reader_helpers/readers_wells.py,sha256=7ja2UJRe2oB3a4LReDfrt6rAEdNnFyUB9-pBqFKfYUc,392
 subsurface/core/structs/__init__.py,sha256=e0kDVRU-5aHrVGnHrjplXDr_HFcIAnd_coFC5cc-ytg,172
 subsurface/core/structs/base_structures/__init__.py,sha256=K3eZixAH9bbN156a7OS9mS-qd3pmBZrrOn1y9ISTHJI,92
+subsurface/core/structs/base_structures/_aux.py,sha256=lJ40ELPHoZRDvXjBZd1j3r_ajtzt5q9IoDJYmcdGH1U,2415
 subsurface/core/structs/base_structures/_liquid_earth_mesh.py,sha256=ZIGLdxbOyC0avIXR6w5JMhk08JtPKJDnGd2Athtx7DM,5729
 subsurface/core/structs/base_structures/_unstructured_data_constructor.py,sha256=nSsmRqyGyrU5DKb0YQKy6FwZm6GVBTPwwTLZJsXPcyk,2671
 subsurface/core/structs/base_structures/base_structures_enum.py,sha256=_B1rsaTnPw6mJhYea0ZIfKmaF3mfkojh-3N5hGG6o5w,90
 subsurface/core/structs/base_structures/structured_data.py,sha256=N6KcAeZJSfd4Wa0PID8aOcw9IIXrNRZ_DspBzF8JPTY,10310
-subsurface/core/structs/base_structures/unstructured_data.py,sha256=bBorNn800ttGMk8MGIgcE2nv8XT6p0FYetpWxShNqlQ,12585
+subsurface/core/structs/base_structures/unstructured_data.py,sha256=-o7XIq886MU_uJHCLFCFklQLNjyLeAx05-cAFMT5y9w,13274
 subsurface/core/structs/structured_elements/__init__.py,sha256=wQ8z6vioC98TNwnqMHlDMVFJ1yOKsmlVa6kHL1SOfZQ,43
 subsurface/core/structs/structured_elements/octree_mesh.py,sha256=3WIgKGPJ3xjjV06gGlLuW7W7POfsJi2z7p4egYD-Y7s,230
 subsurface/core/structs/structured_elements/structured_grid.py,sha256=S08sbGOu-r-rosHm6fwpqZgmkujxMMev7Z8WAwlsuak,1743
@@ -62,7 +63,7 @@ subsurface/modules/reader/profiles/profiles_core.py,sha256=tBvNgdvrpUWRIJv4aW3YY
 subsurface/modules/reader/topography/__init__.py,sha256=U41kQFNPpfYV6KJpMnkqgqLkozqXiG4tgV6rj8IW1BU,7
 subsurface/modules/reader/topography/topo_core.py,sha256=EzcRFJ_zBojVtZkZHbYaUpEIyFUiVaf6zeSWMuyAxxk,3442
 subsurface/modules/reader/volume/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-subsurface/modules/reader/volume/read_grav3d.py,sha256=0PNPoWuMAH-5B2KBWUdNLgcnxcSMbaVY0v21KgSllmY,16406
+subsurface/modules/reader/volume/read_grav3d.py,sha256=5-g65mOMYiOiLqGu3_foDZDGFUIiavkKFC7uZ99v4Dk,14493
 subsurface/modules/reader/volume/read_volume.py,sha256=fg928kOBWxGgWnrLdeOvHDRr54cM5nxb_65-lM1BVsk,13581
 subsurface/modules/reader/volume/segy_reader.py,sha256=Yd1fguaKMrgv514Yc8tBm1NxDhWNtI1qOYWWTF_TgPU,3853
 subsurface/modules/reader/volume/seismic.py,sha256=Iy5zKpjVy7vV6lKyfh_MsUpex6yBMGbovu640NlKkMM,4777
@@ -91,8 +92,8 @@ subsurface/modules/writer/to_rex/material_encoder.py,sha256=J5x1PCW2ljw4JZXLvefG
 subsurface/modules/writer/to_rex/mesh_encoder.py,sha256=dTGqHGbJKgtPgrrG2lrks5r8timfzluqj7JLMC-EBWQ,6291
 subsurface/modules/writer/to_rex/to_rex.py,sha256=dFCCWudTUzZebNrPxnM353_vaykE8PQobVtBAPQkb3E,3685
 subsurface/modules/writer/to_rex/utils.py,sha256=BmMT49WRvbbSuiW_muIvFm4ILR1vcVqh_J23leiMB44,364
-subsurface_terra-2025.1.0rc16.dist-info/licenses/LICENSE,sha256=QEY_TMj0mh5hY6jh6avflZOz0GmH1PgurVoF3FvwXaY,11403
-subsurface_terra-2025.1.0rc16.dist-info/METADATA,sha256=rPt_SUuyoUbI9IAhvUGH-s1GJcqwavwwoK0KLaPy3NI,6900
-subsurface_terra-2025.1.0rc16.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-subsurface_terra-2025.1.0rc16.dist-info/top_level.txt,sha256=f32R_tUSf83CfkpB4vjv5m2XcD8TmDX9h7F4rnEXt5A,11
-subsurface_terra-2025.1.0rc16.dist-info/RECORD,,
+subsurface_terra-2025.1.0rc17.dist-info/licenses/LICENSE,sha256=QEY_TMj0mh5hY6jh6avflZOz0GmH1PgurVoF3FvwXaY,11403
+subsurface_terra-2025.1.0rc17.dist-info/METADATA,sha256=KdRIAeSl2985ykJvSweVD9Gn1mnwbSnMmiLzH8e_yeg,6900
+subsurface_terra-2025.1.0rc17.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+subsurface_terra-2025.1.0rc17.dist-info/top_level.txt,sha256=f32R_tUSf83CfkpB4vjv5m2XcD8TmDX9h7F4rnEXt5A,11
+subsurface_terra-2025.1.0rc17.dist-info/RECORD,,