subsurface-terra 2025.1.0rc15__py3-none-any.whl → 2025.1.0rc16__py3-none-any.whl

subsurface/modules/reader/wells/DEP/_welly_reader.py

@@ -1,180 +1,180 @@
-import glob
-from typing import List
-
-import warnings
-
-from pandas import DataFrame
-
-from subsurface import optional_requirements
-from subsurface.reader.wells.pandas_to_welly import WellyToSubsurfaceHelper
-import numpy as np
-
-from subsurface.structs.base_structures import UnstructuredData
-
-welly = optional_requirements.require_welly()
-striplog = optional_requirements.require_striplog()
-
-
-def welly_to_subsurface(
-        wts: WellyToSubsurfaceHelper,
-        elev=True,
-        n_vertex_per_well=50,
-        convert_lith=True,
-        table: List[striplog.Component] = None,
-        **kwargs) -> UnstructuredData:
-    """Method to convert well data to `subsurface.UnstructuredData`
-
-    Args:
-        elev (bool): In general the (x, y, z) array of positions will have
-            z as TVD, which is positive down. If `elev` is True, positive
-            will be upwards.
-        n_vertex_per_well (int): Number of vertex used to describe the geometry of the
-         well.
-        return_element (bool): if True return a `subsurface.LineSet` instead
-        convert_lith (bool): if True convert lith from stiplog to curve
-        table (List[Striplog.Component]): List of components to map lithologies
-         to value.
-        **kwargs:
-            `Well.location.trajectory` kwargs
-
-    Returns:
-
-    """
-    vertex = np.zeros((0, 3))
-    cells = np.zeros((0, 2), dtype=int)
-
-    last_index = 0
-    missed_wells = []
-
-    for w in wts.p.get_wells():
-        if well_without_valid_survey(w, missed_wells): continue
-
-        cells, vertex, last_index = vertex_and_cells_from_welly_trajectory(
-            cells, elev, kwargs, last_index, n_vertex_per_well, vertex, w)
-
-        change_curve_basis_to_n_vertex_per_well_inplace(n_vertex_per_well, w, wts)
-
-        # Convert striplog into Curve
-        if convert_lith is True:
-            if 'lith' in w.data:
-                if table is None: table = wts.lith_component_table
-                w.data['lith_log'] = striplog_to_curve_log(n_vertex_per_well, table, w, wts)
-            else:
-                w.data["lith_log"] = welly.Curve(-1 * np.ones(n_vertex_per_well - 1, dtype=int))
-
-            if w.data["lith_log"].shape[0] != n_vertex_per_well - 1:
-                raise ValueError("Cell_attr does not match cells")
-
-    try:
-        df = wts.p.df()
-    except ValueError as e:
-        if 'objects passed' in str(e):
-            df = None
-        else:
-            raise ValueError
-
-    print('The following boreholes failed being processed: ', missed_wells)
-
-    unstructured_data = UnstructuredData.from_array(vertex, cells, df)
-    return unstructured_data
-
-
-def striplog_to_curve_log(n_vertex_per_well, table, w: welly.Well, wts: WellyToSubsurfaceHelper) -> welly.Curve:
-    start, stop, step_size = wts._calculate_basis_parameters(w, n_vertex_per_well - 1)
-    s_log, basis, _table = w.data['lith'].to_log(step_size, start, stop, table=table, return_meta=True)
-    return welly.Curve(s_log, basis)
-
-
-def change_curve_basis_to_n_vertex_per_well_inplace(n_points, w, wts):
-    start, stop, step_size = wts._calculate_basis_parameters(w, n_points)
-    basis = np.arange(start, stop, step_size)
-    w.unify_basis(keys=None, basis=basis)
-
-
-def vertex_and_cells_from_welly_trajectory(
-        cells: np.ndarray, elev: bool,
-        welly_trajectory_kwargs: dict,
-        last_index: int, n_vertex_for_well: int,
-        vertex: np.ndarray, w: welly.Well):
-    try:
-        datum = w.location.datum
-    except AttributeError:
-        datum = None
-
-    xyz = w.location.trajectory(datum=datum, elev=elev, points=n_vertex_for_well, **welly_trajectory_kwargs)  # w.location.position
-    # Make sure deviation is there
-    a = np.arange(0 + last_index, xyz.shape[0] - 1 + last_index, dtype=np.int_)
-    b = np.arange(1 + last_index, xyz.shape[0] + last_index, dtype=np.int_)
-    cells_b = np.vstack([a, b]).T
-
-    vertex = np.vstack((vertex, xyz))
-    cells = np.vstack((cells, cells_b))
-    last_index += xyz.shape[0]
-
-    return cells, vertex, last_index
-
-
-def well_without_valid_survey(w: welly.Well, missed_wells: List[str]):
-    well_without_position = w.location.position is None
-    if well_without_position:
-        warnings.warn(f'At least one of the wells do not have '
-                      'assigned a survey. Borehole name: {w.name}')
-        missed_wells.append(w.name)
-    return well_without_position
-
-
-def _create_welly_well_from_las(well_name: str, las_folder: str):
-    """
-    Add well from welly las file.
-
-    Args:
-        well_name (str): Well name
-        las_folder (str): Path to las file
-
-    Returns:
-
-    """
-
-    def _create_well(uwi: str = 'dummy_uwi'):
-        w = welly.Well()
-        w.location.uwi = well_name
-        w.location.name = well_name
-
-        return w
-
-    well = _create_well(well_name)
-    return add_curves_from_las(well, las_folder)
-
-
-def add_curves_from_las(w: welly.Well, las_folder: str) -> welly.Well:
-    """ Add curves from las file. """
-
-    def _read_curves_to_welly_object(well: welly.Well, curve_path: str = '.') -> welly.Well:
-        las_files = glob.glob(curve_path + '*.las')
-        # throw error if no las files found
-        if len(las_files) == 0:
-            raise Exception('No las files found in ' + curve_path)
-
-        for curve in las_files:
-            well.add_curves_from_las(curve)
-        return well
-
-    _read_curves_to_welly_object(w, curve_path=las_folder)
-
-    w_df = w.df()
-    deviation_df = _make_deviation_df(w_df, inclination_header='IMG_INCL', azimuth_header='IMG_AZ')
-    w.location.add_deviation(deviation_df)
-    return w
-
-
-def _make_deviation_df(well_df: DataFrame, inclination_header: str, azimuth_header: str,
-                       depth_header: str = '', depth_index=True):
-    if depth_index:
-        deviation_data = well_df[[inclination_header, azimuth_header]].to_numpy()
-        deviation_index = well_df.index.to_numpy()
-        deviation_complete = np.insert(deviation_data, 0, deviation_index, axis=1)
-        deviation_complete = deviation_complete[~np.isnan(deviation_complete).any(axis=1), :]
-    else:
-        deviation_complete = well_df[[depth_header, inclination_header, azimuth_header]].to_numpy()
-        deviation_complete = deviation_complete[~np.isnan(deviation_complete).any(axis=1), :]
-    return deviation_complete
+import glob
+from typing import List
+
+import warnings
+
+from pandas import DataFrame
+
+from subsurface import optional_requirements
+from subsurface.reader.wells.pandas_to_welly import WellyToSubsurfaceHelper
+import numpy as np
+
+from subsurface.structs.base_structures import UnstructuredData
+
+welly = optional_requirements.require_welly()
+striplog = optional_requirements.require_striplog()
+
+
+def welly_to_subsurface(
+        wts: WellyToSubsurfaceHelper,
+        elev=True,
+        n_vertex_per_well=50,
+        convert_lith=True,
+        table: List[striplog.Component] = None,
+        **kwargs) -> UnstructuredData:
+    """Method to convert well data to `subsurface.UnstructuredData`
+
+    Args:
+        elev (bool): In general the (x, y, z) array of positions will have
+            z as TVD, which is positive down. If `elev` is True, positive
+            will be upwards.
+        n_vertex_per_well (int): Number of vertex used to describe the geometry of the
+         well.
+        return_element (bool): if True return a `subsurface.LineSet` instead
+        convert_lith (bool): if True convert lith from stiplog to curve
+        table (List[Striplog.Component]): List of components to map lithologies
+         to value.
+        **kwargs:
+            `Well.location.trajectory` kwargs
+
+    Returns:
+
+    """
+    vertex = np.zeros((0, 3))
+    cells = np.zeros((0, 2), dtype=int)
+
+    last_index = 0
+    missed_wells = []
+
+    for w in wts.p.get_wells():
+        if well_without_valid_survey(w, missed_wells): continue
+
+        cells, vertex, last_index = vertex_and_cells_from_welly_trajectory(
+            cells, elev, kwargs, last_index, n_vertex_per_well, vertex, w)
+
+        change_curve_basis_to_n_vertex_per_well_inplace(n_vertex_per_well, w, wts)
+
+        # Convert striplog into Curve
+        if convert_lith is True:
+            if 'lith' in w.data:
+                if table is None: table = wts.lith_component_table
+                w.data['lith_log'] = striplog_to_curve_log(n_vertex_per_well, table, w, wts)
+            else:
+                w.data["lith_log"] = welly.Curve(-1 * np.ones(n_vertex_per_well - 1, dtype=int))
+
+            if w.data["lith_log"].shape[0] != n_vertex_per_well - 1:
+                raise ValueError("Cell_attr does not match cells")
+
+    try:
+        df = wts.p.df()
+    except ValueError as e:
+        if 'objects passed' in str(e):
+            df = None
+        else:
+            raise ValueError
+
+    print('The following boreholes failed being processed: ', missed_wells)
+
+    unstructured_data = UnstructuredData.from_array(vertex, cells, df)
+    return unstructured_data
+
+
+def striplog_to_curve_log(n_vertex_per_well, table, w: welly.Well, wts: WellyToSubsurfaceHelper) -> welly.Curve:
+    start, stop, step_size = wts._calculate_basis_parameters(w, n_vertex_per_well - 1)
+    s_log, basis, _table = w.data['lith'].to_log(step_size, start, stop, table=table, return_meta=True)
+    return welly.Curve(s_log, basis)
+
+
+def change_curve_basis_to_n_vertex_per_well_inplace(n_points, w, wts):
+    start, stop, step_size = wts._calculate_basis_parameters(w, n_points)
+    basis = np.arange(start, stop, step_size)
+    w.unify_basis(keys=None, basis=basis)
+
+
+def vertex_and_cells_from_welly_trajectory(
+        cells: np.ndarray, elev: bool,
+        welly_trajectory_kwargs: dict,
+        last_index: int, n_vertex_for_well: int,
+        vertex: np.ndarray, w: welly.Well):
+    try:
+        datum = w.location.datum
+    except AttributeError:
+        datum = None
+
+    xyz = w.location.trajectory(datum=datum, elev=elev, points=n_vertex_for_well, **welly_trajectory_kwargs)  # w.location.position
+    # Make sure deviation is there
+    a = np.arange(0 + last_index, xyz.shape[0] - 1 + last_index, dtype=np.int_)
+    b = np.arange(1 + last_index, xyz.shape[0] + last_index, dtype=np.int_)
+    cells_b = np.vstack([a, b]).T
+
+    vertex = np.vstack((vertex, xyz))
+    cells = np.vstack((cells, cells_b))
+    last_index += xyz.shape[0]
+
+    return cells, vertex, last_index
+
+
+def well_without_valid_survey(w: welly.Well, missed_wells: List[str]):
+    well_without_position = w.location.position is None
+    if well_without_position:
+        warnings.warn(f'At least one of the wells do not have '
+                      'assigned a survey. Borehole name: {w.name}')
+        missed_wells.append(w.name)
+    return well_without_position
+
+
+def _create_welly_well_from_las(well_name: str, las_folder: str):
+    """
+    Add well from welly las file.
+
+    Args:
+        well_name (str): Well name
+        las_folder (str): Path to las file
+
+    Returns:
+
+    """
+
+    def _create_well(uwi: str = 'dummy_uwi'):
+        w = welly.Well()
+        w.location.uwi = well_name
+        w.location.name = well_name
+
+        return w
+
+    well = _create_well(well_name)
+    return add_curves_from_las(well, las_folder)
+
+
+def add_curves_from_las(w: welly.Well, las_folder: str) -> welly.Well:
+    """ Add curves from las file. """
+
+    def _read_curves_to_welly_object(well: welly.Well, curve_path: str = '.') -> welly.Well:
+        las_files = glob.glob(curve_path + '*.las')
+        # throw error if no las files found
+        if len(las_files) == 0:
+            raise Exception('No las files found in ' + curve_path)
+
+        for curve in las_files:
+            well.add_curves_from_las(curve)
+        return well
+
+    _read_curves_to_welly_object(w, curve_path=las_folder)
+
+    w_df = w.df()
+    deviation_df = _make_deviation_df(w_df, inclination_header='IMG_INCL', azimuth_header='IMG_AZ')
+    w.location.add_deviation(deviation_df)
+    return w
+
+
+def _make_deviation_df(well_df: DataFrame, inclination_header: str, azimuth_header: str,
+                       depth_header: str = '', depth_index=True):
+    if depth_index:
+        deviation_data = well_df[[inclination_header, azimuth_header]].to_numpy()
+        deviation_index = well_df.index.to_numpy()
+        deviation_complete = np.insert(deviation_data, 0, deviation_index, axis=1)
+        deviation_complete = deviation_complete[~np.isnan(deviation_complete).any(axis=1), :]
+    else:
+        deviation_complete = well_df[[depth_header, inclination_header, azimuth_header]].to_numpy()
+        deviation_complete = deviation_complete[~np.isnan(deviation_complete).any(axis=1), :]
+    return deviation_complete