subsurface-terra 2025.1.0rc15__py3-none-any.whl → 2025.1.0rc17__py3-none-any.whl

subsurface/core/geological_formats/boreholes/_map_attrs_to_survey.py

@@ -1,234 +1,236 @@
-import numpy as np
-import pandas as pd
-import xarray as xr
-from scipy.interpolate import interp1d
-from typing import Tuple, Optional, Union, List, Any
-
-from ...structs.base_structures import UnstructuredData
-from ...structs.base_structures._unstructured_data_constructor import raw_attributes_to_dict_data_arrays
-from ...structs.unstructured_elements import LineSet
-
-
-def combine_survey_and_attrs(attrs: pd.DataFrame, survey_trajectory: LineSet,well_id_mapper: dict[str, int]) -> UnstructuredData:
-    # Import moved to top for clarity and possibly avoiding repeated imports if called multiple times
-
-    # Ensure all columns in lith exist in new_attrs, if not, add them as NaN
-    new_attrs = _map_attrs_to_measured_depths(attrs, survey_trajectory, well_id_mapper)
-
-    # Construct the final xarray dict without intermediate variable
-    points_attributes_xarray_dict: dict[str, xr.DataArray] = raw_attributes_to_dict_data_arrays(
-        default_attributes_name="vertex_attrs",
-        n_items=survey_trajectory.data.data["vertex_attrs"].shape[0],  # TODO: Can I look this on new_attrs to remove line 11?
-        dims=["points", "vertex_attr"],
-        raw_attributes=new_attrs
-    )
-
-    # Inline construction of UnstructuredData
-    return UnstructuredData.from_data_arrays_dict(
-        xarray_dict={
-                "vertex"      : survey_trajectory.data.data["vertex"],
-                "cells"       : survey_trajectory.data.data["cells"],
-                "vertex_attrs": points_attributes_xarray_dict["vertex_attrs"],
-                "cell_attrs"  : survey_trajectory.data.data["cell_attrs"]
-        },
-        xarray_attributes=survey_trajectory.data.data.attrs,
-        default_cells_attributes_name=survey_trajectory.data.cells_attr_name,
-        default_points_attributes_name=survey_trajectory.data.vertex_attr_name
-    )
-
-def _prepare_categorical_data(attrs: pd.DataFrame) -> pd.DataFrame:
-    """
-    Prepare categorical data for interpolation by converting categorical columns to numeric IDs.
-
-    Args:
-        attrs: DataFrame containing attribute data
-
-    Returns:
-        Modified DataFrame with categorical data prepared for interpolation
-    """
-    # Create a copy to avoid modifying the original
-    attrs_copy = attrs.copy()
-
-    # If component lith exists but lith_ids doesn't, create lith_ids
-    if 'component lith' in attrs_copy.columns and 'lith_ids' not in attrs_copy.columns:
-        attrs_copy['lith_ids'], _ = pd.factorize(attrs_copy['component lith'], use_na_sentinel=True)
-
-    return attrs_copy
-
-
-def _prepare_new_attributes(attrs: pd.DataFrame, survey_trajectory: LineSet) -> pd.DataFrame:
-    """
-    Prepare the new attributes DataFrame by adding missing columns from attrs.
-
-    Args:
-        attrs: DataFrame containing attribute data
-        survey_trajectory: LineSet containing trajectory data
-
-    Returns:
-        New attributes DataFrame with all necessary columns
-    """
-    # Start with a copy of the existing attributes DataFrame
-    new_attrs = survey_trajectory.data.points_attributes.copy()
-
-    # Add missing columns from attrs, preserving their dtypes
-    for col in attrs.columns.difference(new_attrs.columns):
-        new_attrs[col] = np.nan if pd.api.types.is_numeric_dtype(attrs[col]) else None
-
-    return new_attrs
-
-
-def _get_interpolation_locations(attrs_well: pd.DataFrame, well_name: str) -> np.ndarray:
-    """
-    Determine the locations to use for interpolation based on top and base values.
-
-    Args:
-        attrs_well: DataFrame containing well attribute data
-        well_name: Name of the current well
-
-    Returns:
-        Array of location values to use for interpolation
-    """
-    if "base" not in attrs_well.columns:
-        raise ValueError(f"Base column must be present in the file for well '{well_name}'.")
-    elif "top" not in attrs_well.columns:
-        return attrs_well['base'].values
-    else:
-        return ((attrs_well['top'] + attrs_well['base']) / 2).values
-
-
-def _nearest_neighbor_categorical_interpolation(
-    x_locations: np.ndarray,
-    y_values: np.ndarray,
-    target_depths: np.ndarray
-) -> np.ndarray:
-    """
-    Custom nearest neighbor interpolation for categorical data.
-
-    This function finds the nearest source point for each target point
-    and assigns the corresponding categorical value.
-
-    Args:
-        x_locations: Array of source locations
-        y_values: Array of categorical values at source locations
-        target_depths: Array of target depths for interpolation
-
-    Returns:
-        Array of interpolated categorical values
-    """
-    # Initialize output array with NaN or None values
-    result = np.full(target_depths.shape, np.nan, dtype=object)
-
-    # For each target depth, find the nearest source location
-    for i, depth in enumerate(target_depths):
-        # Calculate distances to all source locations
-        distances = np.abs(x_locations - depth)
-
-        # Find the index of the minimum distance
-        if len(distances) > 0:
-            nearest_idx = np.argmin(distances)
-            result[i] = y_values[nearest_idx]
-
-    return result
-
-
-def _interpolate_attribute(
-    attr_values: pd.Series, 
-    x_locations: np.ndarray, 
-    target_depths: np.ndarray, 
-    column_name: str,
-    is_categorical: bool
-) -> np.ndarray:
-    """
-    Interpolate attribute values to target depths.
-
-    Args:
-        attr_values: Series containing attribute values
-        x_locations: Array of source locations for interpolation
-        target_depths: Array of target depths for interpolation
-        column_name: Name of the column being interpolated
-        is_categorical: Whether the attribute is categorical
-
-    Returns:
-        Array of interpolated values
-    """
-    # For categorical data or specific columns, use custom nearest neighbor interpolation
-    if is_categorical or column_name in ['lith_ids', 'component lith']:
-        return _nearest_neighbor_categorical_interpolation(
-            x_locations=x_locations,
-            y_values=attr_values.values,
-            target_depths=target_depths
-        )
-    else:
-        # For numerical data, use scipy's interp1d with linear interpolation
-        interp_func = interp1d(
-            x=x_locations,
-            y=attr_values.values,
-            bounds_error=False,
-            fill_value=np.nan,
-            kind='linear'
-        )
-        return interp_func(target_depths)
-
-
-def _map_attrs_to_measured_depths(attrs: pd.DataFrame, survey_trajectory: LineSet, well_id_mapper: dict[str, int]) -> pd.DataFrame:
-    """
-    Map attributes to measured depths for each well.
-
-    Args:
-        attrs: DataFrame containing attribute data
-        survey_trajectory: LineSet containing trajectory data
-        well_id_mapper: Dictionary mapping well names to IDs
-
-    Returns:
-        DataFrame with attributes mapped to measured depths
-    """
-    # Extract trajectory data
-    trajectory: xr.DataArray = survey_trajectory.data.data["vertex_attrs"]
-    trajectory_well_id: xr.DataArray = trajectory.sel({'vertex_attr': 'well_id'})
-    measured_depths: np.ndarray = trajectory.sel({'vertex_attr': 'measured_depths'}).values.astype(np.float64)
-
-    # Prepare data
-    attrs: pd.DataFrame = _prepare_categorical_data(attrs)
-    new_attrs: pd.DataFrame = _prepare_new_attributes(attrs, survey_trajectory)
-
-    # Process each well
-    for well_name in well_id_mapper:
-        # Skip wells not in the attributes DataFrame
-        if well_name not in attrs.index:
-            print(f"Well '{well_name}' does not exist in the attributes DataFrame.")
-            continue
-
-        # Get well data
-        attrs_well = attrs.loc[[well_name]]
-        well_id = well_id_mapper.get(well_name)
-        well_mask = (trajectory_well_id == well_id).values
-        well_depths = measured_depths[well_mask]
-
-        # Get interpolation locations
-        interp_locations = _get_interpolation_locations(attrs_well, well_name)
-
-        # Interpolate each attribute
-        for col in attrs_well.columns:
-            # Skip location and ID columns
-            if col in ['top', 'base', 'well_id']:
-                continue
-
-            attr_values = attrs_well[col]
-            is_categorical = attr_values.dtype == 'O' or isinstance(attr_values.dtype, pd.CategoricalDtype)
-
-            # Skip columns that can't be interpolated and aren't categorical
-            if is_categorical and col not in ['lith_ids', 'component lith']:
-                continue
-
-            # Interpolate and assign values
-            interpolated_values = _interpolate_attribute(
-                attr_values, 
-                interp_locations, 
-                well_depths, 
-                col,
-                is_categorical
-            )
-
-            new_attrs.loc[well_mask, col] = interpolated_values
-
-    return new_attrs
+import numpy as np
+import pandas as pd
+import xarray as xr
+from typing import Tuple, Optional, Union, List, Any
+
+from subsurface import optional_requirements
+from ...structs.base_structures import UnstructuredData
+from ...structs.base_structures._unstructured_data_constructor import raw_attributes_to_dict_data_arrays
+from ...structs.unstructured_elements import LineSet
+
+
+def combine_survey_and_attrs(attrs: pd.DataFrame, survey_trajectory: LineSet,well_id_mapper: dict[str, int]) -> UnstructuredData:
+    # Import moved to top for clarity and possibly avoiding repeated imports if called multiple times
+
+    # Ensure all columns in lith exist in new_attrs, if not, add them as NaN
+    new_attrs = _map_attrs_to_measured_depths(attrs, survey_trajectory, well_id_mapper)
+
+    # Construct the final xarray dict without intermediate variable
+    points_attributes_xarray_dict: dict[str, xr.DataArray] = raw_attributes_to_dict_data_arrays(
+        default_attributes_name="vertex_attrs",
+        n_items=survey_trajectory.data.data["vertex_attrs"].shape[0],  # TODO: Can I look this on new_attrs to remove line 11?
+        dims=["points", "vertex_attr"],
+        raw_attributes=new_attrs
+    )
+
+    # Inline construction of UnstructuredData
+    return UnstructuredData.from_data_arrays_dict(
+        xarray_dict={
+                "vertex"      : survey_trajectory.data.data["vertex"],
+                "cells"       : survey_trajectory.data.data["cells"],
+                "vertex_attrs": points_attributes_xarray_dict["vertex_attrs"],
+                "cell_attrs"  : survey_trajectory.data.data["cell_attrs"]
+        },
+        xarray_attributes=survey_trajectory.data.data.attrs,
+        default_cells_attributes_name=survey_trajectory.data.cells_attr_name,
+        default_points_attributes_name=survey_trajectory.data.vertex_attr_name
+    )
+
+
+def _prepare_categorical_data(attrs: pd.DataFrame) -> pd.DataFrame:
+    """
+    Prepare categorical data for interpolation by converting categorical columns to numeric IDs.
+
+    Args:
+        attrs: DataFrame containing attribute data
+
+    Returns:
+        Modified DataFrame with categorical data prepared for interpolation
+    """
+    # Create a copy to avoid modifying the original
+    attrs_copy = attrs.copy()
+
+    # If component lith exists but lith_ids doesn't, create lith_ids
+    if 'component lith' in attrs_copy.columns and 'lith_ids' not in attrs_copy.columns:
+        attrs_copy['lith_ids'], _ = pd.factorize(attrs_copy['component lith'], use_na_sentinel=True)
+
+    return attrs_copy
+
+
+def _prepare_new_attributes(attrs: pd.DataFrame, survey_trajectory: LineSet) -> pd.DataFrame:
+    """
+    Prepare the new attributes DataFrame by adding missing columns from attrs.
+
+    Args:
+        attrs: DataFrame containing attribute data
+        survey_trajectory: LineSet containing trajectory data
+
+    Returns:
+        New attributes DataFrame with all necessary columns
+    """
+    # Start with a copy of the existing attributes DataFrame
+    new_attrs = survey_trajectory.data.points_attributes.copy()
+
+    # Add missing columns from attrs, preserving their dtypes
+    for col in attrs.columns.difference(new_attrs.columns):
+        new_attrs[col] = np.nan if pd.api.types.is_numeric_dtype(attrs[col]) else None
+
+    return new_attrs
+
+
+def _get_interpolation_locations(attrs_well: pd.DataFrame, well_name: str) -> np.ndarray:
+    """
+    Determine the locations to use for interpolation based on top and base values.
+
+    Args:
+        attrs_well: DataFrame containing well attribute data
+        well_name: Name of the current well
+
+    Returns:
+        Array of location values to use for interpolation
+    """
+    if "base" not in attrs_well.columns:
+        raise ValueError(f"Base column must be present in the file for well '{well_name}'.")
+    elif "top" not in attrs_well.columns:
+        return attrs_well['base'].values
+    else:
+        return ((attrs_well['top'] + attrs_well['base']) / 2).values
+
+
+def _nearest_neighbor_categorical_interpolation(
+    x_locations: np.ndarray,
+    y_values: np.ndarray,
+    target_depths: np.ndarray
+) -> np.ndarray:
+    """
+    Custom nearest neighbor interpolation for categorical data.
+
+    This function finds the nearest source point for each target point
+    and assigns the corresponding categorical value.
+
+    Args:
+        x_locations: Array of source locations
+        y_values: Array of categorical values at source locations
+        target_depths: Array of target depths for interpolation
+
+    Returns:
+        Array of interpolated categorical values
+    """
+    # Initialize output array with NaN or None values
+    result = np.full(target_depths.shape, np.nan, dtype=object)
+
+    # For each target depth, find the nearest source location
+    for i, depth in enumerate(target_depths):
+        # Calculate distances to all source locations
+        distances = np.abs(x_locations - depth)
+
+        # Find the index of the minimum distance
+        if len(distances) > 0:
+            nearest_idx = np.argmin(distances)
+            result[i] = y_values[nearest_idx]
+
+    return result
+
+
+def _interpolate_attribute(
+    attr_values: pd.Series, 
+    x_locations: np.ndarray, 
+    target_depths: np.ndarray, 
+    column_name: str,
+    is_categorical: bool
+) -> np.ndarray:
+    """
+    Interpolate attribute values to target depths.
+
+    Args:
+        attr_values: Series containing attribute values
+        x_locations: Array of source locations for interpolation
+        target_depths: Array of target depths for interpolation
+        column_name: Name of the column being interpolated
+        is_categorical: Whether the attribute is categorical
+
+    Returns:
+        Array of interpolated values
+    """
+    # For categorical data or specific columns, use custom nearest neighbor interpolation
+    if is_categorical or column_name in ['lith_ids', 'component lith']:
+        return _nearest_neighbor_categorical_interpolation(
+            x_locations=x_locations,
+            y_values=attr_values.values,
+            target_depths=target_depths
+        )
+    else:
+        # For numerical data, use scipy's interp1d with linear interpolation
+        scipy = optional_requirements.require_scipy()
+        interp_func = scipy.interpolate.interp1d(
+            x=x_locations,
+            y=attr_values.values,
+            bounds_error=False,
+            fill_value=np.nan,
+            kind='linear'
+        )
+        return interp_func(target_depths)
+
+
+def _map_attrs_to_measured_depths(attrs: pd.DataFrame, survey_trajectory: LineSet, well_id_mapper: dict[str, int]) -> pd.DataFrame:
+    """
+    Map attributes to measured depths for each well.
+
+    Args:
+        attrs: DataFrame containing attribute data
+        survey_trajectory: LineSet containing trajectory data
+        well_id_mapper: Dictionary mapping well names to IDs
+
+    Returns:
+        DataFrame with attributes mapped to measured depths
+    """
+    # Extract trajectory data
+    trajectory: xr.DataArray = survey_trajectory.data.data["vertex_attrs"]
+    trajectory_well_id: xr.DataArray = trajectory.sel({'vertex_attr': 'well_id'})
+    measured_depths: np.ndarray = trajectory.sel({'vertex_attr': 'measured_depths'}).values.astype(np.float64)
+
+    # Prepare data
+    attrs: pd.DataFrame = _prepare_categorical_data(attrs)
+    new_attrs: pd.DataFrame = _prepare_new_attributes(attrs, survey_trajectory)
+
+    # Process each well
+    for well_name in well_id_mapper:
+        # Skip wells not in the attributes DataFrame
+        if well_name not in attrs.index:
+            print(f"Well '{well_name}' does not exist in the attributes DataFrame.")
+            continue
+
+        # Get well data
+        attrs_well = attrs.loc[[well_name]]
+        well_id = well_id_mapper.get(well_name)
+        well_mask = (trajectory_well_id == well_id).values
+        well_depths = measured_depths[well_mask]
+
+        # Get interpolation locations
+        interp_locations = _get_interpolation_locations(attrs_well, well_name)
+
+        # Interpolate each attribute
+        for col in attrs_well.columns:
+            # Skip location and ID columns
+            if col in ['top', 'base', 'well_id']:
+                continue
+
+            attr_values = attrs_well[col]
+            is_categorical = attr_values.dtype == 'O' or isinstance(attr_values.dtype, pd.CategoricalDtype)
+
+            # Skip columns that can't be interpolated and aren't categorical
+            if is_categorical and col not in ['lith_ids', 'component lith']:
+                continue
+
+            # Interpolate and assign values
+            interpolated_values = _interpolate_attribute(
+                attr_values, 
+                interp_locations, 
+                well_depths, 
+                col,
+                is_categorical
+            )
+
+            new_attrs.loc[well_mask, col] = interpolated_values
+
+    return new_attrs