subsurface-terra 2025.1.0rc18__py3-none-any.whl → 2025.1.0rc19__py3-none-any.whl

subsurface/__init__.py

@@ -1,31 +1,31 @@
-import subsurface.modules.reader
-import subsurface.api.interfaces
-import subsurface.modules.writer
-from . import core
-from .modules import visualization
-from subsurface.core.structs import *
-from datetime import datetime
-import dotenv
-
-dotenv.load_dotenv()
-
-try:
-    from subsurface import visualization
-except ImportError:
-    pass
-try:
-    from importlib.metadata import version, PackageNotFoundError
-except ImportError:  # For Python <3.8, fallback
-    from importlib_metadata import version, PackageNotFoundError
-    
-# Version.
-try:
-    __version__ = version("subsurface")  # Use package name
-except ImportError:
-    # If it was not installed, then we don't know the version. We could throw a
-    # warning here, but this case *should* be rare. subsurface should be
-    # installed properly!
-    __version__ = 'unknown-'+datetime.today().strftime('%Y%m%d')
-
-if __name__ == '__main__':
-    pass
+import subsurface.modules.reader
+import subsurface.api.interfaces
+import subsurface.modules.writer
+from . import core
+from .modules import visualization
+from subsurface.core.structs import *
+from datetime import datetime
+import dotenv
+
+dotenv.load_dotenv()
+
+try:
+    from subsurface import visualization
+except ImportError:
+    pass
+try:
+    from importlib.metadata import version, PackageNotFoundError
+except ImportError:  # For Python <3.8, fallback
+    from importlib_metadata import version, PackageNotFoundError
+    
+# Version.
+try:
+    __version__ = version("subsurface")  # Use package name
+except ImportError:
+    # If it was not installed, then we don't know the version. We could throw a
+    # warning here, but this case *should* be rare. subsurface should be
+    # installed properly!
+    __version__ = 'unknown-'+datetime.today().strftime('%Y%m%d')
+
+if __name__ == '__main__':
+    pass

subsurface/_version.py

@@ -1,34 +1,34 @@
-# file generated by setuptools-scm
-# don't change, don't track in version control
-
-__all__ = [
-    "__version__",
-    "__version_tuple__",
-    "version",
-    "version_tuple",
-    "__commit_id__",
-    "commit_id",
-]
-
-TYPE_CHECKING = False
-if TYPE_CHECKING:
-    from typing import Tuple
-    from typing import Union
-
-    VERSION_TUPLE = Tuple[Union[int, str], ...]
-    COMMIT_ID = Union[str, None]
-else:
-    VERSION_TUPLE = object
-    COMMIT_ID = object
-
-version: str
-__version__: str
-__version_tuple__: VERSION_TUPLE
-version_tuple: VERSION_TUPLE
-commit_id: COMMIT_ID
-__commit_id__: COMMIT_ID
-
-__version__ = version = '2025.1.0rc18'
-__version_tuple__ = version_tuple = (2025, 1, 0, 'rc18')
-
-__commit_id__ = commit_id = None
+# file generated by setuptools-scm
+# don't change, don't track in version control
+
+__all__ = [
+    "__version__",
+    "__version_tuple__",
+    "version",
+    "version_tuple",
+    "__commit_id__",
+    "commit_id",
+]
+
+TYPE_CHECKING = False
+if TYPE_CHECKING:
+    from typing import Tuple
+    from typing import Union
+
+    VERSION_TUPLE = Tuple[Union[int, str], ...]
+    COMMIT_ID = Union[str, None]
+else:
+    VERSION_TUPLE = object
+    COMMIT_ID = object
+
+version: str
+__version__: str
+__version_tuple__: VERSION_TUPLE
+version_tuple: VERSION_TUPLE
+commit_id: COMMIT_ID
+__commit_id__: COMMIT_ID
+
+__version__ = version = '2025.1.0rc19'
+__version_tuple__ = version_tuple = (2025, 1, 0, 'rc19')
+
+__commit_id__ = commit_id = None

subsurface/api/__init__.py

@@ -1,13 +1,13 @@
-from .interfaces.stream import (
-    DXF_stream_to_unstruc,
-    OMF_stream_to_unstruc,
-    CSV_wells_stream_to_unstruc,
-    CSV_mesh_stream_to_unstruc,
-    CSV_volume_stream_to_unstruc,
-    CSV_volume_stream_to_struct,
-    VTK_stream_to_struct,  
-    MX_stream_to_unstruc,
-    OBJ_stream_to_trisurf,
-    GLTF_stream_to_trisurf,
-    MSH_stream_to_struct,
-)
+from .interfaces.stream import (
+    DXF_stream_to_unstruc,
+    OMF_stream_to_unstruc,
+    CSV_wells_stream_to_unstruc,
+    CSV_mesh_stream_to_unstruc,
+    CSV_volume_stream_to_unstruc,
+    CSV_volume_stream_to_struct,
+    VTK_stream_to_struct,  
+    MX_stream_to_unstruc,
+    OBJ_stream_to_trisurf,
+    GLTF_stream_to_trisurf,
+    MSH_stream_to_struct,
+)

subsurface/api/interfaces/__init__.py

@@ -1,3 +1,3 @@
-
-
-
+
+
+

subsurface/api/interfaces/stream.py

@@ -1,136 +1,136 @@
-import io
-from io import BytesIO
-from typing import TextIO, Optional
-
-import pandas
-
-from ...core.structs import TriSurf
-from ...core.reader_helpers.reader_unstruct import ReaderUnstructuredHelper
-from ...core.reader_helpers.readers_data import GenericReaderFilesHelper
-from ...core.geological_formats import BoreholeSet
-from ...core.structs.base_structures import UnstructuredData, StructuredData
-
-from ...modules import reader
-from ...modules.reader.mesh._trimesh_reader import TriMeshTransformations
-from ...modules.reader.volume.read_volume import read_volumetric_mesh_to_subsurface, read_VTK_structured_grid
-from ...modules.reader.mesh.surfaces_api import read_2d_mesh_to_unstruct
-from ...modules.reader.volume.volume_utils import interpolate_unstructured_data_to_structured_data
-
-from ..reader.read_wells import read_wells
-
-
-def DXF_stream_to_unstruc(stream: TextIO) -> UnstructuredData:
-    vertex, cells, cell_attr_int, cell_attr_map = reader.dxf_stream_to_unstruct_input(stream)
-
-    unstruct = UnstructuredData.from_array(
-        vertex,
-        cells,
-        cells_attr=pandas.DataFrame(cell_attr_int, columns=["Id"]),
-        xarray_attributes={"cell_attr_map": cell_attr_map},
-    )
-
-    return unstruct
-
-
-def OMF_stream_to_unstruc(stream: BytesIO) -> list[UnstructuredData]:
-    list_unstruct: list[UnstructuredData] = reader.omf_stream_to_unstructs(stream)
-    return list_unstruct
-
-
-def MX_stream_to_unstruc(stream: TextIO) -> list[UnstructuredData]:
-    list_unstruct: list[UnstructuredData] = [reader.mx_to_unstruc_from_binary(stream)]
-    return list_unstruct
-
-
-def OBJ_stream_to_trisurf(obj_stream: TextIO, mtl_stream: list[TextIO],
-                          texture_stream: list[io.BytesIO], coordinate_system: TriMeshTransformations) -> TriSurf:
-    tri_mesh: TriSurf = reader.load_obj_with_trimesh_from_binary(
-        obj_stream=obj_stream,
-        mtl_stream=mtl_stream,
-        texture_stream=texture_stream,
-        coord_system=coordinate_system
-    )
-    return tri_mesh
-
-
-def GLTF_stream_to_trisurf(gltf_stream: io.BytesIO, coordinate_system: TriMeshTransformations) -> TriSurf:
-    tri_mesh: TriSurf = reader.load_gltf_with_trimesh(gltf_stream, coordinate_system)
-    return tri_mesh
-
-
-def VTK_stream_to_struct(stream: BytesIO, attribute_name: str) -> list[StructuredData]:
-    struct = read_VTK_structured_grid(stream, attribute_name)
-    return [struct]
-
-
-def MSH_stream_to_struct(grid_stream: TextIO, values_stream: TextIO, missing_value: Optional[float], attr_name: Optional[str]) -> list[StructuredData]:
-    struct = reader.read_msh_structured_grid(grid_stream, values_stream, missing_value, attr_name)
-    return [struct]
-
-
-def CSV_wells_stream_to_unstruc(
-        collars_reader: GenericReaderFilesHelper,
-        surveys_reader: GenericReaderFilesHelper,
-        attrs_reader: GenericReaderFilesHelper,
-        is_lith_attr: bool,
-        number_nodes: int,
-        add_attrs_as_nodes: bool,
-        duplicate_attr_depths: bool
-) -> list[UnstructuredData]:
-    borehole_set: BoreholeSet = read_wells(
-        collars_reader=collars_reader,
-        surveys_reader=surveys_reader,
-        attrs_reader=attrs_reader,
-        is_lith_attr=is_lith_attr,
-        number_nodes=number_nodes,
-        add_attrs_as_nodes=add_attrs_as_nodes,
-        duplicate_attr_depths=duplicate_attr_depths
-    )
-
-    list_unstruct: list[UnstructuredData] = [
-            borehole_set.collars.data,
-            borehole_set.combined_trajectory.data
-    ]
-    return list_unstruct
-
-
-def CSV_mesh_stream_to_unstruc(
-        vertex_reader: GenericReaderFilesHelper,
-        edges_reader: GenericReaderFilesHelper,
-        cells_attrs_reader: GenericReaderFilesHelper,
-        vertex_attrs_reader: GenericReaderFilesHelper
-) -> list[UnstructuredData]:
-    reader_unstruc = ReaderUnstructuredHelper(vertex_reader, edges_reader, vertex_attrs_reader, cells_attrs_reader)
-    ud = read_2d_mesh_to_unstruct(reader_unstruc)
-    return [ud]
-
-
-def CSV_volume_stream_to_unstruc(
-        coord_reader: GenericReaderFilesHelper,
-        attrs_reader: GenericReaderFilesHelper
-) -> list[UnstructuredData]:
-    ud = read_volumetric_mesh_to_subsurface(
-        reader_helper_coord=coord_reader,
-        reader_helper_attr=attrs_reader
-    )
-    return [ud]
-
-
-def CSV_volume_stream_to_struct(
-        coord_reader: GenericReaderFilesHelper,
-        attrs_reader: GenericReaderFilesHelper,
-        attr_name: str,
-        resolution: list[int]
-) -> list[StructuredData]:
-    ud = read_volumetric_mesh_to_subsurface(
-        reader_helper_coord=coord_reader,
-        reader_helper_attr=attrs_reader
-    )
-
-    sd: StructuredData = interpolate_unstructured_data_to_structured_data(
-        ud=ud,
-        attr_name=attr_name,
-        resolution=resolution
-    )
-
-    return [sd]
+import io
+from io import BytesIO
+from typing import TextIO, Optional
+
+import pandas
+
+from ...core.structs import TriSurf
+from ...core.reader_helpers.reader_unstruct import ReaderUnstructuredHelper
+from ...core.reader_helpers.readers_data import GenericReaderFilesHelper
+from ...core.geological_formats import BoreholeSet
+from ...core.structs.base_structures import UnstructuredData, StructuredData
+
+from ...modules import reader
+from ...modules.reader.mesh._trimesh_reader import TriMeshTransformations
+from ...modules.reader.volume.read_volume import read_volumetric_mesh_to_subsurface, read_VTK_structured_grid
+from ...modules.reader.mesh.surfaces_api import read_2d_mesh_to_unstruct
+from ...modules.reader.volume.volume_utils import interpolate_unstructured_data_to_structured_data
+
+from ..reader.read_wells import read_wells
+
+
+def DXF_stream_to_unstruc(stream: TextIO) -> UnstructuredData:
+    vertex, cells, cell_attr_int, cell_attr_map = reader.dxf_stream_to_unstruct_input(stream)
+
+    unstruct = UnstructuredData.from_array(
+        vertex,
+        cells,
+        cells_attr=pandas.DataFrame(cell_attr_int, columns=["Id"]),
+        xarray_attributes={"cell_attr_map": cell_attr_map},
+    )
+
+    return unstruct
+
+
+def OMF_stream_to_unstruc(stream: BytesIO) -> list[UnstructuredData]:
+    list_unstruct: list[UnstructuredData] = reader.omf_stream_to_unstructs(stream)
+    return list_unstruct
+
+
+def MX_stream_to_unstruc(stream: TextIO) -> list[UnstructuredData]:
+    list_unstruct: list[UnstructuredData] = [reader.mx_to_unstruc_from_binary(stream)]
+    return list_unstruct
+
+
+def OBJ_stream_to_trisurf(obj_stream: TextIO, mtl_stream: list[TextIO],
+                          texture_stream: list[io.BytesIO], coordinate_system: TriMeshTransformations) -> TriSurf:
+    tri_mesh: TriSurf = reader.load_obj_with_trimesh_from_binary(
+        obj_stream=obj_stream,
+        mtl_stream=mtl_stream,
+        texture_stream=texture_stream,
+        coord_system=coordinate_system
+    )
+    return tri_mesh
+
+
+def GLTF_stream_to_trisurf(gltf_stream: io.BytesIO, coordinate_system: TriMeshTransformations) -> TriSurf:
+    tri_mesh: TriSurf = reader.load_gltf_with_trimesh(gltf_stream, coordinate_system)
+    return tri_mesh
+
+
+def VTK_stream_to_struct(stream: BytesIO, attribute_name: str) -> list[StructuredData]:
+    struct = read_VTK_structured_grid(stream, attribute_name)
+    return [struct]
+
+
+def MSH_stream_to_struct(grid_stream: TextIO, values_stream: TextIO, missing_value: Optional[float], attr_name: Optional[str]) -> list[StructuredData]:
+    struct = reader.read_msh_structured_grid(grid_stream, values_stream, missing_value, attr_name)
+    return [struct]
+
+
+def CSV_wells_stream_to_unstruc(
+        collars_reader: GenericReaderFilesHelper,
+        surveys_reader: GenericReaderFilesHelper,
+        attrs_reader: GenericReaderFilesHelper,
+        is_lith_attr: bool,
+        number_nodes: int,
+        add_attrs_as_nodes: bool,
+        duplicate_attr_depths: bool
+) -> list[UnstructuredData]:
+    borehole_set: BoreholeSet = read_wells(
+        collars_reader=collars_reader,
+        surveys_reader=surveys_reader,
+        attrs_reader=attrs_reader,
+        is_lith_attr=is_lith_attr,
+        number_nodes=number_nodes,
+        add_attrs_as_nodes=add_attrs_as_nodes,
+        duplicate_attr_depths=duplicate_attr_depths
+    )
+
+    list_unstruct: list[UnstructuredData] = [
+            borehole_set.collars.data,
+            borehole_set.combined_trajectory.data
+    ]
+    return list_unstruct
+
+
+def CSV_mesh_stream_to_unstruc(
+        vertex_reader: GenericReaderFilesHelper,
+        edges_reader: GenericReaderFilesHelper,
+        cells_attrs_reader: GenericReaderFilesHelper,
+        vertex_attrs_reader: GenericReaderFilesHelper
+) -> list[UnstructuredData]:
+    reader_unstruc = ReaderUnstructuredHelper(vertex_reader, edges_reader, vertex_attrs_reader, cells_attrs_reader)
+    ud = read_2d_mesh_to_unstruct(reader_unstruc)
+    return [ud]
+
+
+def CSV_volume_stream_to_unstruc(
+        coord_reader: GenericReaderFilesHelper,
+        attrs_reader: GenericReaderFilesHelper
+) -> list[UnstructuredData]:
+    ud = read_volumetric_mesh_to_subsurface(
+        reader_helper_coord=coord_reader,
+        reader_helper_attr=attrs_reader
+    )
+    return [ud]
+
+
+def CSV_volume_stream_to_struct(
+        coord_reader: GenericReaderFilesHelper,
+        attrs_reader: GenericReaderFilesHelper,
+        attr_name: str,
+        resolution: list[int]
+) -> list[StructuredData]:
+    ud = read_volumetric_mesh_to_subsurface(
+        reader_helper_coord=coord_reader,
+        reader_helper_attr=attrs_reader
+    )
+
+    sd: StructuredData = interpolate_unstructured_data_to_structured_data(
+        ud=ud,
+        attr_name=attr_name,
+        resolution=resolution
+    )
+
+    return [sd]

subsurface/api/reader/read_wells.py

@@ -1,78 +1,78 @@
-from subsurface.core.geological_formats.boreholes.boreholes import MergeOptions
-
-from subsurface.core.structs.base_structures.base_structures_enum import SpecialCellCase
-
-from subsurface.core.structs import UnstructuredData, PointSet
-
-from subsurface import optional_requirements
-from subsurface.modules.reader.wells.read_borehole_interface import read_collar, read_survey, read_lith, read_attributes
-
-from subsurface.core.geological_formats import BoreholeSet, Collars, Survey
-
-from subsurface.core.reader_helpers.readers_data import GenericReaderFilesHelper
-
-
-def read_wells(
-        collars_reader: GenericReaderFilesHelper,
-        surveys_reader: GenericReaderFilesHelper,
-        attrs_reader: GenericReaderFilesHelper,
-        is_lith_attr: bool,
-        number_nodes: int = 10,
-        add_attrs_as_nodes: bool = False,
-        duplicate_attr_depths: bool = False 
-) -> BoreholeSet:
-    # ! FIGUROUT IF WE NEED LITH
-    
-    
-    pd = optional_requirements.require_pandas()
-    try:
-        collar_df: pd.DataFrame = read_collar(collars_reader)
-        unstruc: UnstructuredData = UnstructuredData.from_array(
-            vertex=collar_df[["x", "y", "z"]].values,
-            cells=SpecialCellCase.POINTS
-        )
-        points = PointSet(data=unstruc)
-        collars: Collars = Collars(
-            ids=collar_df.index.to_list(),
-            collar_loc=points
-        )
-    except KeyError as e:
-        raise ValueError(f"Error while reading collars: {e}. Check if the columns are named x, y, z or use Columns Map.")
-    except Exception as e:
-        raise ValueError(f"Error while reading collars: {e}")   
-    
-    try:
-        survey_df: pd.DataFrame = read_survey(surveys_reader)
-    except Exception as e:
-        raise ValueError(f"Error while reading surveys: {e}")
-    
-    try:
-        attrs: pd.DataFrame = read_attributes(attrs_reader, is_lith=is_lith_attr)
-    except Exception as e:
-        raise ValueError(f"Error while reading attributes: {e}")
-    
-    try:
-        if add_attrs_as_nodes:
-            attr_df = attrs
-        else:
-            attr_df = None
-
-        survey: Survey = Survey.from_df(
-            survey_df=survey_df,
-            attr_df=attr_df,
-            number_nodes=number_nodes,
-            duplicate_attr_depths=duplicate_attr_depths
-        )
-
-        # Check if component lith is in columns or columns_map
-        survey.update_survey_with_lith(attrs)
-    except Exception as e:
-        raise ValueError(f"Error while creating survey: {e}")
-
-    borehole_set = BoreholeSet(
-        collars=collars,
-        survey=survey,
-        merge_option=MergeOptions.INTERSECT
-    )
-
-    return borehole_set
+from subsurface.core.geological_formats.boreholes.boreholes import MergeOptions
+
+from subsurface.core.structs.base_structures.base_structures_enum import SpecialCellCase
+
+from subsurface.core.structs import UnstructuredData, PointSet
+
+from subsurface import optional_requirements
+from subsurface.modules.reader.wells.read_borehole_interface import read_collar, read_survey, read_lith, read_attributes
+
+from subsurface.core.geological_formats import BoreholeSet, Collars, Survey
+
+from subsurface.core.reader_helpers.readers_data import GenericReaderFilesHelper
+
+
+def read_wells(
+        collars_reader: GenericReaderFilesHelper,
+        surveys_reader: GenericReaderFilesHelper,
+        attrs_reader: GenericReaderFilesHelper,
+        is_lith_attr: bool,
+        number_nodes: int = 10,
+        add_attrs_as_nodes: bool = False,
+        duplicate_attr_depths: bool = False 
+) -> BoreholeSet:
+    # ! FIGUROUT IF WE NEED LITH
+    
+    
+    pd = optional_requirements.require_pandas()
+    try:
+        collar_df: pd.DataFrame = read_collar(collars_reader)
+        unstruc: UnstructuredData = UnstructuredData.from_array(
+            vertex=collar_df[["x", "y", "z"]].values,
+            cells=SpecialCellCase.POINTS
+        )
+        points = PointSet(data=unstruc)
+        collars: Collars = Collars(
+            ids=collar_df.index.to_list(),
+            collar_loc=points
+        )
+    except KeyError as e:
+        raise ValueError(f"Error while reading collars: {e}. Check if the columns are named x, y, z or use Columns Map.")
+    except Exception as e:
+        raise ValueError(f"Error while reading collars: {e}")   
+    
+    try:
+        survey_df: pd.DataFrame = read_survey(surveys_reader)
+    except Exception as e:
+        raise ValueError(f"Error while reading surveys: {e}")
+    
+    try:
+        attrs: pd.DataFrame = read_attributes(attrs_reader, is_lith=is_lith_attr)
+    except Exception as e:
+        raise ValueError(f"Error while reading attributes: {e}")
+    
+    try:
+        if add_attrs_as_nodes:
+            attr_df = attrs
+        else:
+            attr_df = None
+
+        survey: Survey = Survey.from_df(
+            survey_df=survey_df,
+            attr_df=attr_df,
+            number_nodes=number_nodes,
+            duplicate_attr_depths=duplicate_attr_depths
+        )
+
+        # Check if component lith is in columns or columns_map
+        survey.update_survey_with_lith(attrs)
+    except Exception as e:
+        raise ValueError(f"Error while creating survey: {e}")
+
+    borehole_set = BoreholeSet(
+        collars=collars,
+        survey=survey,
+        merge_option=MergeOptions.INTERSECT
+    )
+
+    return borehole_set