subsurface-terra 2026.1.1rc1__py3-none-any.whl → 2026.1.2rc1__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 = '2026.1.1rc1'
-__version_tuple__ = version_tuple = (2026, 1, 1, 'rc1')
+__version__ = version = '2026.1.2rc1'
+__version_tuple__ = version_tuple = (2026, 1, 2, 'rc1')
 
 __commit_id__ = commit_id = None

subsurface/core/geological_formats/boreholes/_survey_to_unstruct.py

@@ -47,7 +47,10 @@ def data_frame_to_unstructured_data(survey_df: 'pd.DataFrame', number_nodes: int
 
         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)
+        measured_depths = _calculate_distances(
+            array_of_vertices=this_well_vertex,
+            start_md = depths[0]
+        )
 
         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_)
@@ -152,12 +155,12 @@ def _grab_depths_from_attr(
     return attr_depths
 
 
-def _calculate_distances(array_of_vertices: np.ndarray) -> np.ndarray:
+def _calculate_distances(array_of_vertices: np.ndarray, start_md: float = 0) -> 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)
+    # Start from start_md instead of 0
+    measured_depths = np.insert(np.cumsum(distances) + start_md, 0, start_md)
     return measured_depths

subsurface/modules/reader/topography/topo_core.py

@@ -11,7 +11,7 @@ from ....core.reader_helpers.reader_unstruct import ReaderUnstructuredHelper
 from ..mesh.surfaces_api import read_2d_mesh_to_unstruct
 
 
-def read_structured_topography(path, crop_to_extent: Optional[Sequence]=None) -> StructuredData:
+def read_structured_topography(path, crop_to_extent: Optional[Sequence] = None) -> StructuredData:
     rasterio = require_rasterio()
 
     extension = get_extension(path)
@@ -31,8 +31,34 @@ def read_structured_topography_to_unstructured(path) -> UnstructuredData:
     return topography_to_unstructured_data(structured_data)
 
 
-def rasterio_dataset_to_structured_data(dataset, crop_to_extent: Optional[Sequence]=None):
-    if crop_to_extent is not None: 
+def rasterio_dataset_to_structured_data(dataset, crop_to_extent: Optional[Sequence] = None):
+    rasterio = require_rasterio()
+
+    if crop_to_extent is not None:
+        window = _get_raster_window(crop_to_extent, dataset)
+    else:
+        window = None
+
+    data = dataset.read(1, window=window)
+    data = np.fliplr(data.T)
+    shape = data.shape
+
+    # Use window bounds if cropping, otherwise use full dataset bounds
+    if window is not None:
+        left, bottom, right, top = rasterio.windows.bounds(window, dataset.transform)
+    else:
+        left, bottom, right, top = dataset.bounds.left, dataset.bounds.bottom, dataset.bounds.right, dataset.bounds.top
+
+    coords = {
+            'x': np.linspace(left, right, shape[0]),
+            'y': np.linspace(bottom, top, shape[1])
+    }
+    structured_data = StructuredData.from_numpy(data, data_array_name='topography', coords=coords)
+    return structured_data
+
+
+def rasterio_dataset_to_structured_data_(dataset, crop_to_extent: Optional[Sequence] = None):
+    if crop_to_extent is not None:
         window = _get_raster_window(crop_to_extent, dataset)
     else:
         window = None
@@ -40,30 +66,30 @@ def rasterio_dataset_to_structured_data(dataset, crop_to_extent: Optional[Sequen
     data = dataset.read(1, window=window)
     data = np.fliplr(data.T)
     shape = data.shape
-    
+
     # TODO: ===================
     # TODO: Add the option to crop
     # TODO: Resample
-    
+
     coords = {
-        'x': np.linspace(
-            dataset.bounds.left,
-            dataset.bounds.right,
-            shape[0]
-        ),
-        'y': np.linspace(
-            dataset.bounds.bottom,
-            dataset.bounds.top,
-            shape[1]
-        )
+            'x': np.linspace(
+                dataset.bounds.left,
+                dataset.bounds.right,
+                shape[0]
+            ),
+            'y': np.linspace(
+                dataset.bounds.bottom,
+                dataset.bounds.top,
+                shape[1]
+            )
     }
     structured_data = StructuredData.from_numpy(data, data_array_name='topography', coords=coords)
     return structured_data
 
 
-def read_unstructured_topography(path, additional_reader_kwargs: Optional[dict]=None) -> UnstructuredData:
+def read_unstructured_topography(path, additional_reader_kwargs: Optional[dict] = None) -> UnstructuredData:
     """For example, a dxf file"""
-    
+
     additional_reader_kwargs = additional_reader_kwargs or {}
     helper = GenericReaderFilesHelper(
         file_or_buffer=path,

subsurface/modules/reader/wells/_read_to_df.py

@@ -21,7 +21,12 @@ def check_format_and_read_to_df(reader_helper: GenericReaderFilesHelper) -> pd.D
             )
         case (bytes() | io.BytesIO() | io.StringIO() | io.TextIOWrapper()), _:
             reader = _get_reader(reader_helper.format)
-            d = reader(reader_helper.file_or_buffer, **reader_helper.pandas_reader_kwargs)
+            d = reader(
+                filepath_or_buffer=reader_helper.file_or_buffer,
+                sep=reader_helper.separator,
+                engine='python',
+                **reader_helper.pandas_reader_kwargs
+            )
         case dict(), _:
             reader = _get_reader('dict')
             d = reader(reader_helper.file_or_buffer)

{subsurface_terra-2026.1.1rc1.dist-info → subsurface_terra-2026.1.2rc1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: subsurface_terra
-Version: 2026.1.1rc1
+Version: 2026.1.2rc1
 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-2026.1.1rc1.dist-info → subsurface_terra-2026.1.2rc1.dist-info}/RECORD

@@ -1,5 +1,5 @@
 subsurface/__init__.py,sha256=7_KttQl8rZeJG2AIZUEA_oXRWZYkJ6DUqKjqlLgF9cA,899
-subsurface/_version.py,sha256=x_XUkgur2S5FBHy9HGt2HBG6flOou1FypU142m3se8w,720
+subsurface/_version.py,sha256=tE78uKXzXCH9s4NPbDhW9zz9Qd46coDQ2Jr5voEKWms,720
 subsurface/optional_requirements.py,sha256=SLaMSoiGTx8ea8rpHee4Zs4te0BXcxxDWC4SF0g0RuE,2767
 subsurface/api/__init__.py,sha256=Lfx7Dq0GzQsea19w8YO4v1ZSmgeLRgR6IvjvDDjjpDY,356
 subsurface/api/interfaces/__init__.py,sha256=ajz1GSNU9xYVrFEDSz6Xwg7amWQ_yvW75tQa1ZvRIWc,3
@@ -12,7 +12,7 @@ subsurface/core/geological_formats/fault.py,sha256=Rsy8uvtOQCd9qxI6pfNDNE9DE3XTY
 subsurface/core/geological_formats/boreholes/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 subsurface/core/geological_formats/boreholes/_combine_trajectories.py,sha256=2CC_zp_ZpWw7RM7vSbFRWWpTYchs0h6Qagm-HumqJyw,5129
 subsurface/core/geological_formats/boreholes/_map_attrs_to_survey.py,sha256=BC143dgj6DzBmAerqDzo6pfqU1gUh3cQe6_LrZDnaSY,9230
-subsurface/core/geological_formats/boreholes/_survey_to_unstruct.py,sha256=toQvj1rgkucYyvjSlh0zsbP3fcJAXLCYLIbZh-boSsU,6430
+subsurface/core/geological_formats/boreholes/_survey_to_unstruct.py,sha256=aSzUmGa1qRU8tef5BaUiicf4gINvPYs9dpu0aUw_nrE,6483
 subsurface/core/geological_formats/boreholes/boreholes.py,sha256=wFeyT_G4N8bh6eYGQshOic_2bs8OGIv32Kr7SrSI5r4,6405
 subsurface/core/geological_formats/boreholes/collars.py,sha256=JdcrIy1JN7QS6gL1SzzqUwelanIX8geAH4r57HdhdGA,724
 subsurface/core/geological_formats/boreholes/survey.py,sha256=ajb0Y9nylmIiK9J3MyGF8kDp5MO5MdH-Z62-ubbOrbM,3500
@@ -61,7 +61,7 @@ subsurface/modules/reader/petrel/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRk
 subsurface/modules/reader/profiles/__init__.py,sha256=ajz1GSNU9xYVrFEDSz6Xwg7amWQ_yvW75tQa1ZvRIWc,3
 subsurface/modules/reader/profiles/profiles_core.py,sha256=tBvNgdvrpUWRIJv4aW3YYcnX7tJAup10fIOSCRB3zto,6371
 subsurface/modules/reader/topography/__init__.py,sha256=U41kQFNPpfYV6KJpMnkqgqLkozqXiG4tgV6rj8IW1BU,7
-subsurface/modules/reader/topography/topo_core.py,sha256=EzcRFJ_zBojVtZkZHbYaUpEIyFUiVaf6zeSWMuyAxxk,3442
+subsurface/modules/reader/topography/topo_core.py,sha256=qwNamnsY5_Uy7z51BtgOt7Yz7_7Qfe_UZrcwDlvaq1U,4397
 subsurface/modules/reader/volume/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 subsurface/modules/reader/volume/read_grav3d.py,sha256=5-g65mOMYiOiLqGu3_foDZDGFUIiavkKFC7uZ99v4Dk,14493
 subsurface/modules/reader/volume/read_volume.py,sha256=W1meuMPbkW8S3Nh7KN2DnNWNFoHHgOp0kv7GQkL7oM8,4386
@@ -69,7 +69,7 @@ subsurface/modules/reader/volume/segy_reader.py,sha256=Yd1fguaKMrgv514Yc8tBm1NxD
 subsurface/modules/reader/volume/seismic.py,sha256=Iy5zKpjVy7vV6lKyfh_MsUpex6yBMGbovu640NlKkMM,4777
 subsurface/modules/reader/volume/volume_utils.py,sha256=7Ih6JLrMRotQHO9g0bS43IgsefpiXwcx79EKUBDLhdE,1324
 subsurface/modules/reader/wells/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-subsurface/modules/reader/wells/_read_to_df.py,sha256=bAfh-K372qXwRDEBYIyS4Vy1qOg1OYaOXjGDQoa0fx0,2270
+subsurface/modules/reader/wells/_read_to_df.py,sha256=uYv2iHH_C9MgTGTqS5igKpOVGAgg6MJhVVzwNbwIWZE,2413
 subsurface/modules/reader/wells/read_borehole_interface.py,sha256=9b9evxY7HScOF51Iaa7Om3ImQypaSBuoCx8uV53oQeI,5751
 subsurface/modules/reader/wells/wells_utils.py,sha256=46o3mm9hpreaeo4P7izx7tLC6wGyynRMUU1JMnK9930,2138
 subsurface/modules/reader/wells/DEP/__init__.py,sha256=IV0_m6AY2NM-IVImhBZnLmIaQIzunt7wg79sqPrxV2I,1844
@@ -92,8 +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-2026.1.1rc1.dist-info/licenses/LICENSE,sha256=QEY_TMj0mh5hY6jh6avflZOz0GmH1PgurVoF3FvwXaY,11403
-subsurface_terra-2026.1.1rc1.dist-info/METADATA,sha256=BGDU1h_Urn7IMMscBrp8tpM7mSobDMcDsxWEd58_Jxg,6977
-subsurface_terra-2026.1.1rc1.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-subsurface_terra-2026.1.1rc1.dist-info/top_level.txt,sha256=f32R_tUSf83CfkpB4vjv5m2XcD8TmDX9h7F4rnEXt5A,11
-subsurface_terra-2026.1.1rc1.dist-info/RECORD,,
+subsurface_terra-2026.1.2rc1.dist-info/licenses/LICENSE,sha256=QEY_TMj0mh5hY6jh6avflZOz0GmH1PgurVoF3FvwXaY,11403
+subsurface_terra-2026.1.2rc1.dist-info/METADATA,sha256=idGw-WWnxpPtY4_q2ur3ZMvNyHy-PuMVv0j0oXilJko,6977
+subsurface_terra-2026.1.2rc1.dist-info/WHEEL,sha256=wUyA8OaulRlbfwMtmQsvNngGrxQHAvkKcvRmdizlJi0,92
+subsurface_terra-2026.1.2rc1.dist-info/top_level.txt,sha256=f32R_tUSf83CfkpB4vjv5m2XcD8TmDX9h7F4rnEXt5A,11
+subsurface_terra-2026.1.2rc1.dist-info/RECORD,,

{subsurface_terra-2026.1.1rc1.dist-info → subsurface_terra-2026.1.2rc1.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (80.9.0)
+Generator: setuptools (80.10.2)
 Root-Is-Purelib: true
 Tag: py3-none-any