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

subsurface/core/geological_formats/boreholes/_survey_to_unstruct.py

@@ -1,163 +1,163 @@
-from typing import Hashable, Optional
-
-import numpy as np
-import pandas as pd
-
-from subsurface import optional_requirements
-from ...structs.base_structures import UnstructuredData
-
-
-def data_frame_to_unstructured_data(survey_df: 'pd.DataFrame', number_nodes: int, attr_df: Optional['pd.DataFrame'] = None,
-                                     duplicate_attr_depths: bool = False) -> UnstructuredData:
-    wp = optional_requirements.require_wellpathpy()
-
-    cum_vertex: np.ndarray = np.empty((0, 3), dtype=np.float32)
-    cells: np.ndarray = np.empty((0, 2), dtype=np.int_)
-    cell_attr: pd.DataFrame = pd.DataFrame(columns=['well_id'], dtype=np.float32)
-    vertex_attr: pd.DataFrame = pd.DataFrame()
-
-    for e, (borehole_id, data) in enumerate(survey_df.groupby(level=0)):
-        dev = wp.deviation(
-            md=data['md'].values,
-            inc=data['inc'].values,
-            azi=data['azi'].values
-        )
-
-        md_min = dev.md.min()
-        md_max = dev.md.max()
-
-        attr_depths = _grab_depths_from_attr(
-            attr_df=attr_df,
-            borehole_id=borehole_id,
-            duplicate_attr_depths=duplicate_attr_depths,
-            md_max=md_max,
-            md_min=md_min
-        )
-
-        # Now combine attr_depths with depths
-        md_min = dev.md.min()
-        md_max = dev.md.max()
-        depths = np.linspace(md_min, md_max, number_nodes)
-        depths = np.union1d(depths, attr_depths)
-        depths.sort()
-
-        # Resample positions at depths
-        pos = dev.minimum_curvature().resample(depths=depths)
-        vertex_count = cum_vertex.shape[0]
-
-        this_well_vertex = np.vstack([pos.easting, pos.northing, pos.depth]).T
-        cum_vertex = np.vstack([cum_vertex, this_well_vertex])
-        measured_depths = _calculate_distances(array_of_vertices=this_well_vertex)
-
-        n_vertex_shift_0 = np.arange(0, len(pos.depth) - 1, dtype=np.int_)
-        n_vertex_shift_1 = np.arange(1, len(pos.depth), dtype=np.int_)
-        cell_per_well = np.vstack([n_vertex_shift_0, n_vertex_shift_1]).T + vertex_count
-        cells = np.vstack([cells, cell_per_well])
-
-        attribute_values = np.isin(depths, attr_depths)
-
-        vertex_attr_per_well = pd.DataFrame({
-                'well_id'        : [e] * len(pos.depth),
-                'measured_depths': measured_depths,
-                'is_attr_point'  : attribute_values,
-        })
-
-        vertex_attr = pd.concat([vertex_attr, vertex_attr_per_well], ignore_index=True)
-
-        # Add the id (e), to cell_attr
-        cell_attr = pd.concat([cell_attr, pd.DataFrame({'well_id': [e] * len(cell_per_well)})], ignore_index=True)
-
-    unstruct = UnstructuredData.from_array(
-        vertex=cum_vertex,
-        cells=cells.astype(int),
-        vertex_attr=vertex_attr.reset_index(drop=True),
-        cells_attr=cell_attr.reset_index(drop=True)
-    )
-
-    unstruct.data.attrs["well_id_mapper"] = {well_id: e for e, well_id in enumerate(survey_df.index.unique(level=0))}
-
-    return unstruct
-
-
-def _grab_depths_from_attr(
-        attr_df: pd.DataFrame,
-        borehole_id: Hashable,
-        duplicate_attr_depths: bool,
-        md_max: float,
-        md_min: float
-) -> np.ndarray:
-    # Initialize attr_depths and attr_labels as empty arrays
-    attr_depths = np.array([], dtype=float)
-    attr_labels = np.array([], dtype='<U4')  # Initialize labels for 'top' and 'base'
-
-    if attr_df is None or ("top" not in attr_df.columns and "base" not in attr_df.columns):
-        return attr_depths
-
-    try:
-        vals = attr_df.loc[borehole_id]
-
-        tops = np.array([], dtype=float)
-        bases = np.array([], dtype=float)
-
-        if 'top' in vals:
-            if isinstance(vals, pd.DataFrame):
-                tops = vals['top'].values.flatten()
-            else:
-                tops = np.array([vals['top']])
-            # Convert to float and remove NaNs
-            tops = tops.astype(float)
-            tops = tops[~np.isnan(tops)]
-            # Clip to within md range
-            tops = tops[(tops >= md_min) & (tops <= md_max)]
-
-        if 'base' in vals:
-            if isinstance(vals, pd.DataFrame):
-                bases = vals['base'].values.flatten()
-            else:
-                bases = np.array([vals['base']])
-            # Convert to float and remove NaNs
-            bases = bases.astype(float)
-            bases = bases[~np.isnan(bases)]
-            # Clip to within md range
-            bases = bases[(bases >= md_min) & (bases <= md_max)]
-
-        # Combine tops and bases into attr_depths with labels
-        attr_depths = np.concatenate((tops, bases))
-        attr_labels = np.array(['top'] * len(tops) + ['base'] * len(bases))
-
-        # Drop duplicates while preserving order
-        _, unique_indices = np.unique(attr_depths, return_index=True)
-        attr_depths = attr_depths[unique_indices]
-        attr_labels = attr_labels[unique_indices]
-
-    except KeyError:
-        # No attributes for this borehole_id or missing columns
-        attr_depths = np.array([], dtype=float)
-        attr_labels = np.array([], dtype='<U4')
-
-    # If duplicate_attr_depths is True, duplicate attr_depths with a tiny offset
-    if duplicate_attr_depths and len(attr_depths) > 0:
-        tiny_offset = (md_max - md_min) * 1e-6  # A tiny fraction of the depth range
-        # Create offsets: +tiny_offset for 'top', -tiny_offset for 'base'
-        offsets = np.where(attr_labels == 'top', tiny_offset, -tiny_offset)
-        duplicated_attr_depths = attr_depths + offsets
-        # Ensure the duplicated depths are within the md range
-        valid_indices = (duplicated_attr_depths >= md_min) & (duplicated_attr_depths <= md_max)
-        duplicated_attr_depths = duplicated_attr_depths[valid_indices]
-        # Original attribute depths
-        original_attr_depths = attr_depths
-        # Combine originals and duplicates
-        attr_depths = np.hstack([original_attr_depths, duplicated_attr_depths])
-
-    return attr_depths
-
-
-def _calculate_distances(array_of_vertices: np.ndarray) -> np.ndarray:
-    # Calculate the differences between consecutive points
-    differences = np.diff(array_of_vertices, axis=0)
-
-    # Calculate the Euclidean distance for each pair of consecutive points
-    distances = np.linalg.norm(differences, axis=1)
-    # Insert a 0 at the beginning to represent the starting point at the surface
-    measured_depths = np.insert(np.cumsum(distances), 0, 0)
-    return measured_depths
+from typing import Hashable, Optional
+
+import numpy as np
+import pandas as pd
+
+from subsurface import optional_requirements
+from ...structs.base_structures import UnstructuredData
+
+
+def data_frame_to_unstructured_data(survey_df: 'pd.DataFrame', number_nodes: int, attr_df: Optional['pd.DataFrame'] = None,
+                                     duplicate_attr_depths: bool = False) -> UnstructuredData:
+    wp = optional_requirements.require_wellpathpy()
+
+    cum_vertex: np.ndarray = np.empty((0, 3), dtype=np.float32)
+    cells: np.ndarray = np.empty((0, 2), dtype=np.int_)
+    cell_attr: pd.DataFrame = pd.DataFrame(columns=['well_id'], dtype=np.float32)
+    vertex_attr: pd.DataFrame = pd.DataFrame()
+
+    for e, (borehole_id, data) in enumerate(survey_df.groupby(level=0)):
+        dev = wp.deviation(
+            md=data['md'].values,
+            inc=data['inc'].values,
+            azi=data['azi'].values
+        )
+
+        md_min = dev.md.min()
+        md_max = dev.md.max()
+
+        attr_depths = _grab_depths_from_attr(
+            attr_df=attr_df,
+            borehole_id=borehole_id,
+            duplicate_attr_depths=duplicate_attr_depths,
+            md_max=md_max,
+            md_min=md_min
+        )
+
+        # Now combine attr_depths with depths
+        md_min = dev.md.min()
+        md_max = dev.md.max()
+        depths = np.linspace(md_min, md_max, number_nodes)
+        depths = np.union1d(depths, attr_depths)
+        depths.sort()
+
+        # Resample positions at depths
+        pos = dev.minimum_curvature().resample(depths=depths)
+        vertex_count = cum_vertex.shape[0]
+
+        this_well_vertex = np.vstack([pos.easting, pos.northing, pos.depth]).T
+        cum_vertex = np.vstack([cum_vertex, this_well_vertex])
+        measured_depths = _calculate_distances(array_of_vertices=this_well_vertex)
+
+        n_vertex_shift_0 = np.arange(0, len(pos.depth) - 1, dtype=np.int_)
+        n_vertex_shift_1 = np.arange(1, len(pos.depth), dtype=np.int_)
+        cell_per_well = np.vstack([n_vertex_shift_0, n_vertex_shift_1]).T + vertex_count
+        cells = np.vstack([cells, cell_per_well])
+
+        attribute_values = np.isin(depths, attr_depths)
+
+        vertex_attr_per_well = pd.DataFrame({
+                'well_id'        : [e] * len(pos.depth),
+                'measured_depths': measured_depths,
+                'is_attr_point'  : attribute_values,
+        })
+
+        vertex_attr = pd.concat([vertex_attr, vertex_attr_per_well], ignore_index=True)
+
+        # Add the id (e), to cell_attr
+        cell_attr = pd.concat([cell_attr, pd.DataFrame({'well_id': [e] * len(cell_per_well)})], ignore_index=True)
+
+    unstruct = UnstructuredData.from_array(
+        vertex=cum_vertex,
+        cells=cells.astype(int),
+        vertex_attr=vertex_attr.reset_index(drop=True),
+        cells_attr=cell_attr.reset_index(drop=True)
+    )
+
+    unstruct.data.attrs["well_id_mapper"] = {well_id: e for e, well_id in enumerate(survey_df.index.unique(level=0))}
+
+    return unstruct
+
+
+def _grab_depths_from_attr(
+        attr_df: pd.DataFrame,
+        borehole_id: Hashable,
+        duplicate_attr_depths: bool,
+        md_max: float,
+        md_min: float
+) -> np.ndarray:
+    # Initialize attr_depths and attr_labels as empty arrays
+    attr_depths = np.array([], dtype=float)
+    attr_labels = np.array([], dtype='<U4')  # Initialize labels for 'top' and 'base'
+
+    if attr_df is None or ("top" not in attr_df.columns and "base" not in attr_df.columns):
+        return attr_depths
+
+    try:
+        vals = attr_df.loc[borehole_id]
+
+        tops = np.array([], dtype=float)
+        bases = np.array([], dtype=float)
+
+        if 'top' in vals:
+            if isinstance(vals, pd.DataFrame):
+                tops = vals['top'].values.flatten()
+            else:
+                tops = np.array([vals['top']])
+            # Convert to float and remove NaNs
+            tops = tops.astype(float)
+            tops = tops[~np.isnan(tops)]
+            # Clip to within md range
+            tops = tops[(tops >= md_min) & (tops <= md_max)]
+
+        if 'base' in vals:
+            if isinstance(vals, pd.DataFrame):
+                bases = vals['base'].values.flatten()
+            else:
+                bases = np.array([vals['base']])
+            # Convert to float and remove NaNs
+            bases = bases.astype(float)
+            bases = bases[~np.isnan(bases)]
+            # Clip to within md range
+            bases = bases[(bases >= md_min) & (bases <= md_max)]
+
+        # Combine tops and bases into attr_depths with labels
+        attr_depths = np.concatenate((tops, bases))
+        attr_labels = np.array(['top'] * len(tops) + ['base'] * len(bases))
+
+        # Drop duplicates while preserving order
+        _, unique_indices = np.unique(attr_depths, return_index=True)
+        attr_depths = attr_depths[unique_indices]
+        attr_labels = attr_labels[unique_indices]
+
+    except KeyError:
+        # No attributes for this borehole_id or missing columns
+        attr_depths = np.array([], dtype=float)
+        attr_labels = np.array([], dtype='<U4')
+
+    # If duplicate_attr_depths is True, duplicate attr_depths with a tiny offset
+    if duplicate_attr_depths and len(attr_depths) > 0:
+        tiny_offset = (md_max - md_min) * 1e-6  # A tiny fraction of the depth range
+        # Create offsets: +tiny_offset for 'top', -tiny_offset for 'base'
+        offsets = np.where(attr_labels == 'top', tiny_offset, -tiny_offset)
+        duplicated_attr_depths = attr_depths + offsets
+        # Ensure the duplicated depths are within the md range
+        valid_indices = (duplicated_attr_depths >= md_min) & (duplicated_attr_depths <= md_max)
+        duplicated_attr_depths = duplicated_attr_depths[valid_indices]
+        # Original attribute depths
+        original_attr_depths = attr_depths
+        # Combine originals and duplicates
+        attr_depths = np.hstack([original_attr_depths, duplicated_attr_depths])
+
+    return attr_depths
+
+
+def _calculate_distances(array_of_vertices: np.ndarray) -> np.ndarray:
+    # Calculate the differences between consecutive points
+    differences = np.diff(array_of_vertices, axis=0)
+
+    # Calculate the Euclidean distance for each pair of consecutive points
+    distances = np.linalg.norm(differences, axis=1)
+    # Insert a 0 at the beginning to represent the starting point at the surface
+    measured_depths = np.insert(np.cumsum(distances), 0, 0)
+    return measured_depths

subsurface/core/geological_formats/boreholes/boreholes.py

@@ -1,140 +1,140 @@
-import numpy as np
-import pandas as pd
-from dataclasses import dataclass
-from typing import Hashable, Literal
-
-from ._combine_trajectories import create_combined_trajectory, MergeOptions
-from .collars import Collars
-from .survey import Survey
-from ...structs import LineSet
-
-
-@dataclass
-class BoreholeSet:
-    """
-    This module provides a class, `BoreholeSet`, that represents a collection of boreholes. It contains methods for accessing coordinate data for each lithology in the boreholes.
-    
-    Notes: 
-        - Collars is defined as 1 UnstructuredData
-        - Combined trajectory is defined as 1 UnstructuredData
-
-    Classes:
-        - `BoreholeSet`: Represents a collection of boreholes.
-
-    Methods:
-        - `__init__`: Initializes a new `BoreholeSet` object with the specified input parameters.
-        - `get_top_coords_for_each_lith`: Returns a dictionary of top coordinates for each lithology in the boreholes.
-        - `get_bottom_coords_for_each_lith`: Returns a dictionary of bottom coordinates for each lithology in the boreholes.
-
-    Attributes:
-        - `collars`: A `Collars` object representing the collar information for the boreholes.
-        - `survey`: A `Survey` object representing the survey information for the boreholes.
-        - `combined_trajectory`: A `LineSet` object representing the combined trajectory of the boreholes.
-
-    Usage:
-        ```
-        borehole_set = BoreholeSet(collars, survey, merge_option)
-        top_coords = borehole_set.get_top_coords_for_each_lith()
-        bottom_coords = borehole_set.get_bottom_coords_for_each_lith()
-        ```
-
-    Note: The example usage code provided above is for demonstration purposes only. Please replace `collars`, `survey`, and `merge_option` with the actual input parameters when using the `BoreholeSet` class.
-
-    """
-    __slots__ = ['collars', 'survey', 'combined_trajectory']
-    collars: Collars
-    survey: Survey
-    combined_trajectory: LineSet
-
-    def __init__(self, collars: Collars, survey: Survey, merge_option: MergeOptions, slice_=slice(None)):
-
-        new_collars = self._remap_collars_with_survey(collars, survey)
-
-        self.collars = new_collars
-        self.survey = survey
-        self.combined_trajectory: LineSet = create_combined_trajectory(collars, survey, merge_option, slice_)
-
-    @staticmethod
-    def _remap_collars_with_survey(collars, survey):
-        import pandas as pd
-        # Create a DataFrame from your first list
-        df1 = pd.DataFrame({'name': collars.ids, 'x': collars.data.vertex[:, 0], 'y': collars.data.vertex[:, 1], 'z': collars.data.vertex[:, 2]})
-        df1 = df1.set_index('name')
-        # Reindex to match the second list of names
-        df_reindexed = df1.reindex(survey.well_id_mapper.keys())
-        new_collars = Collars.from_df(df_reindexed)
-        return new_collars
-
-    def to_binary(self, path: str) -> bool:
-        # I need to implement the survey to and then name the files accordingly
-        bytearray_le_collars: bytes = self.collars.data.to_binary()
-        bytearray_le_trajectory: bytes = self.combined_trajectory.data.to_binary()
-
-        new_file = open(f"{path}_collars.le", "wb")
-        new_file.write(bytearray_le_collars)
-
-        new_file = open(f"{path}_trajectory.le", "wb")
-        new_file.write(bytearray_le_trajectory)
-        return True
-
-    def get_top_coords_for_each_lith(self) -> dict[Hashable, np.ndarray]:
-        merged_df = self._merge_vertex_data_arrays_to_dataframe()
-        component_lith_arrays = {}
-        for lith, group in merged_df.groupby('lith_ids'):
-            lith = int(lith)
-            first_vertices = group.groupby('well_id').first().reset_index()
-            array = first_vertices[['X', 'Y', 'Z']].values
-            component_lith_arrays[lith] = array
-
-        return component_lith_arrays
-
-    def get_bottom_coords_for_each_lith(self, group_by: Literal['component lith', 'lith_ids'] = 'lith_ids') -> dict[Hashable, np.ndarray]:
-        """
-        Retrieves the bottom coordinates for each lithological component or lith ID from
-        the merged vertex data arrays.
-
-        This function groups the merged data by either 'component lith' or 'lith_ids',
-        then extracts the coordinates of the bottommost vertices for each well. It
-        returns a dictionary where keys are either lithological component identifiers
-        or lith IDs, and values are arrays of 3D coordinates representing the bottom
-        vertices.
-
-        Args:
-            group_by (Literal['component lith', 'lith_ids']): Specifies the grouping
-                column to use for lithological components. Acceptable values are either
-                'component lith' or 'lith_ids'. Defaults to 'lith_ids'.
-
-        Returns:
-            dict[Hashable, np.ndarray]: A dictionary mapping the lithological component
-            or lith ID to an array of 3D coordinates ([X, Y, Z]) corresponding to the
-            bottom vertices for each well.
-
-        Raises:
-            ValueError: If no groups are found from the specified `group_by` column.
-        """
-        merged_df = self._merge_vertex_data_arrays_to_dataframe()
-        component_lith_arrays = {}
-        group = merged_df.groupby(group_by)
-
-        if group.ngroups == 0:
-            raise ValueError("No components found")
-        for lith, group in group:
-            lith = int(lith)
-            first_vertices = group.groupby('well_id').last().reset_index()
-            array = first_vertices[['X', 'Y', 'Z']].values
-            component_lith_arrays[lith] = array
-
-        return component_lith_arrays
-
-    def _merge_vertex_data_arrays_to_dataframe(self):
-        ds = self.combined_trajectory.data.data
-        # Convert vertex attributes to a DataFrame for easier manipulation
-        vertex_attrs_df = ds['vertex_attrs'].to_dataframe().reset_index()
-        vertex_attrs_df = vertex_attrs_df.pivot(index='points', columns='vertex_attr', values='vertex_attrs').reset_index()
-        # Convert vertex coordinates to a DataFrame
-        vertex_df = ds['vertex'].to_dataframe().reset_index()
-        vertex_df = vertex_df.pivot(index='points', columns='XYZ', values='vertex').reset_index()
-        # Merge the attributes with the vertex coordinates
-        merged_df = pd.merge(vertex_df, vertex_attrs_df, on='points')
-        # Create a dictionary to hold the numpy arrays for each component lith
-        return merged_df
+import numpy as np
+import pandas as pd
+from dataclasses import dataclass
+from typing import Hashable, Literal
+
+from ._combine_trajectories import create_combined_trajectory, MergeOptions
+from .collars import Collars
+from .survey import Survey
+from ...structs import LineSet
+
+
+@dataclass
+class BoreholeSet:
+    """
+    This module provides a class, `BoreholeSet`, that represents a collection of boreholes. It contains methods for accessing coordinate data for each lithology in the boreholes.
+    
+    Notes: 
+        - Collars is defined as 1 UnstructuredData
+        - Combined trajectory is defined as 1 UnstructuredData
+
+    Classes:
+        - `BoreholeSet`: Represents a collection of boreholes.
+
+    Methods:
+        - `__init__`: Initializes a new `BoreholeSet` object with the specified input parameters.
+        - `get_top_coords_for_each_lith`: Returns a dictionary of top coordinates for each lithology in the boreholes.
+        - `get_bottom_coords_for_each_lith`: Returns a dictionary of bottom coordinates for each lithology in the boreholes.
+
+    Attributes:
+        - `collars`: A `Collars` object representing the collar information for the boreholes.
+        - `survey`: A `Survey` object representing the survey information for the boreholes.
+        - `combined_trajectory`: A `LineSet` object representing the combined trajectory of the boreholes.
+
+    Usage:
+        ```
+        borehole_set = BoreholeSet(collars, survey, merge_option)
+        top_coords = borehole_set.get_top_coords_for_each_lith()
+        bottom_coords = borehole_set.get_bottom_coords_for_each_lith()
+        ```
+
+    Note: The example usage code provided above is for demonstration purposes only. Please replace `collars`, `survey`, and `merge_option` with the actual input parameters when using the `BoreholeSet` class.
+
+    """
+    __slots__ = ['collars', 'survey', 'combined_trajectory']
+    collars: Collars
+    survey: Survey
+    combined_trajectory: LineSet
+
+    def __init__(self, collars: Collars, survey: Survey, merge_option: MergeOptions, slice_=slice(None)):
+
+        new_collars = self._remap_collars_with_survey(collars, survey)
+
+        self.collars = new_collars
+        self.survey = survey
+        self.combined_trajectory: LineSet = create_combined_trajectory(collars, survey, merge_option, slice_)
+
+    @staticmethod
+    def _remap_collars_with_survey(collars, survey):
+        import pandas as pd
+        # Create a DataFrame from your first list
+        df1 = pd.DataFrame({'name': collars.ids, 'x': collars.data.vertex[:, 0], 'y': collars.data.vertex[:, 1], 'z': collars.data.vertex[:, 2]})
+        df1 = df1.set_index('name')
+        # Reindex to match the second list of names
+        df_reindexed = df1.reindex(survey.well_id_mapper.keys())
+        new_collars = Collars.from_df(df_reindexed)
+        return new_collars
+
+    def to_binary(self, path: str) -> bool:
+        # I need to implement the survey to and then name the files accordingly
+        bytearray_le_collars: bytes = self.collars.data.to_binary()
+        bytearray_le_trajectory: bytes = self.combined_trajectory.data.to_binary()
+
+        new_file = open(f"{path}_collars.le", "wb")
+        new_file.write(bytearray_le_collars)
+
+        new_file = open(f"{path}_trajectory.le", "wb")
+        new_file.write(bytearray_le_trajectory)
+        return True
+
+    def get_top_coords_for_each_lith(self) -> dict[Hashable, np.ndarray]:
+        merged_df = self._merge_vertex_data_arrays_to_dataframe()
+        component_lith_arrays = {}
+        for lith, group in merged_df.groupby('lith_ids'):
+            lith = int(lith)
+            first_vertices = group.groupby('well_id').first().reset_index()
+            array = first_vertices[['X', 'Y', 'Z']].values
+            component_lith_arrays[lith] = array
+
+        return component_lith_arrays
+
+    def get_bottom_coords_for_each_lith(self, group_by: Literal['component lith', 'lith_ids'] = 'lith_ids') -> dict[Hashable, np.ndarray]:
+        """
+        Retrieves the bottom coordinates for each lithological component or lith ID from
+        the merged vertex data arrays.
+
+        This function groups the merged data by either 'component lith' or 'lith_ids',
+        then extracts the coordinates of the bottommost vertices for each well. It
+        returns a dictionary where keys are either lithological component identifiers
+        or lith IDs, and values are arrays of 3D coordinates representing the bottom
+        vertices.
+
+        Args:
+            group_by (Literal['component lith', 'lith_ids']): Specifies the grouping
+                column to use for lithological components. Acceptable values are either
+                'component lith' or 'lith_ids'. Defaults to 'lith_ids'.
+
+        Returns:
+            dict[Hashable, np.ndarray]: A dictionary mapping the lithological component
+            or lith ID to an array of 3D coordinates ([X, Y, Z]) corresponding to the
+            bottom vertices for each well.
+
+        Raises:
+            ValueError: If no groups are found from the specified `group_by` column.
+        """
+        merged_df = self._merge_vertex_data_arrays_to_dataframe()
+        component_lith_arrays = {}
+        group = merged_df.groupby(group_by)
+
+        if group.ngroups == 0:
+            raise ValueError("No components found")
+        for lith, group in group:
+            lith = int(lith)
+            first_vertices = group.groupby('well_id').last().reset_index()
+            array = first_vertices[['X', 'Y', 'Z']].values
+            component_lith_arrays[lith] = array
+
+        return component_lith_arrays
+
+    def _merge_vertex_data_arrays_to_dataframe(self):
+        ds = self.combined_trajectory.data.data
+        # Convert vertex attributes to a DataFrame for easier manipulation
+        vertex_attrs_df = ds['vertex_attrs'].to_dataframe().reset_index()
+        vertex_attrs_df = vertex_attrs_df.pivot(index='points', columns='vertex_attr', values='vertex_attrs').reset_index()
+        # Convert vertex coordinates to a DataFrame
+        vertex_df = ds['vertex'].to_dataframe().reset_index()
+        vertex_df = vertex_df.pivot(index='points', columns='XYZ', values='vertex').reset_index()
+        # Merge the attributes with the vertex coordinates
+        merged_df = pd.merge(vertex_df, vertex_attrs_df, on='points')
+        # Create a dictionary to hold the numpy arrays for each component lith
+        return merged_df