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

subsurface/modules/reader/read_netcdf.py

@@ -1,38 +1,38 @@
-import warnings
-
-import xarray as xr
-
-from subsurface import UnstructuredData, StructuredData
-
-
-__all__ = ['read_unstruct', 'read_struct']
-
-
-def read_unstruct(path, legacy=False, **kwargs):
-    ds = xr.open_dataset(path, **kwargs)
-
-    if legacy is False:
-        try:
-            ud = UnstructuredData(ds)
-        except KeyError:
-            warnings.warn("Trying loading legacy files.")
-            ud = read_unstruct(path, legacy=True)
-    else:
-        ud = _legacy_read_unstruct(ds)
-    return ud
-
-
-def _legacy_read_unstruct(ds):
-    xarray_dict = {
-        "vertex": ds.vertex,
-        "cells": ds.cells,
-        "cell_attrs": ds.attributes.rename({"attribute": "cell_attr"}),
-        "vertex_attrs": ds.points_attributes.rename({"points_attribute": "vertex_attr"})
-    }
-    ud = UnstructuredData.from_data_arrays_dict(xarray_dict, ds.coords, ds.attrs)
-    return ud
-
-
-def read_struct(path, **kwargs):
-    ds = xr.open_dataset(path, **kwargs)
-    return StructuredData(ds)
+import warnings
+
+import xarray as xr
+
+from subsurface import UnstructuredData, StructuredData
+
+
+__all__ = ['read_unstruct', 'read_struct']
+
+
+def read_unstruct(path, legacy=False, **kwargs):
+    ds = xr.open_dataset(path, **kwargs)
+
+    if legacy is False:
+        try:
+            ud = UnstructuredData(ds)
+        except KeyError:
+            warnings.warn("Trying loading legacy files.")
+            ud = read_unstruct(path, legacy=True)
+    else:
+        ud = _legacy_read_unstruct(ds)
+    return ud
+
+
+def _legacy_read_unstruct(ds):
+    xarray_dict = {
+        "vertex": ds.vertex,
+        "cells": ds.cells,
+        "cell_attrs": ds.attributes.rename({"attribute": "cell_attr"}),
+        "vertex_attrs": ds.points_attributes.rename({"points_attribute": "vertex_attr"})
+    }
+    ud = UnstructuredData.from_data_arrays_dict(xarray_dict, ds.coords, ds.attrs)
+    return ud
+
+
+def read_struct(path, **kwargs):
+    ds = xr.open_dataset(path, **kwargs)
+    return StructuredData(ds)

subsurface/modules/reader/topography/__init__.py

@@ -1,7 +1,7 @@
-
-
-
-
-
-
-
+
+
+
+
+
+
+

subsurface/modules/reader/topography/topo_core.py

@@ -1,100 +1,100 @@
-from typing import Sequence, Optional
-
-import numpy as np
-
-from ....core.structs.structured_elements.structured_grid import StructuredGrid
-from ....optional_requirements import require_rasterio
-from ....core.structs import StructuredData, UnstructuredData
-from ....core.utils.utils_core import get_extension
-from ....core.reader_helpers.readers_data import GenericReaderFilesHelper
-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:
-    rasterio = require_rasterio()
-
-    extension = get_extension(path)
-    if extension == '.tif':
-        structured_data = rasterio_dataset_to_structured_data(
-            dataset=rasterio.open(path),
-            crop_to_extent=crop_to_extent
-        )
-    else:
-        raise NotImplementedError('The extension given cannot be read yet')
-
-    return structured_data
-
-
-def read_structured_topography_to_unstructured(path) -> UnstructuredData:
-    structured_data = read_structured_topography(path)
-    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: 
-        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
-    
-    # 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]
-        )
-    }
-    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:
-    """For example, a dxf file"""
-    
-    additional_reader_kwargs = additional_reader_kwargs or {}
-    helper = GenericReaderFilesHelper(
-        file_or_buffer=path,
-        additional_reader_kwargs=additional_reader_kwargs or {}
-    )
-    unstructured_helper = ReaderUnstructuredHelper(helper)
-    unstruct: UnstructuredData = read_2d_mesh_to_unstruct(unstructured_helper)
-    return unstruct
-
-
-def topography_to_unstructured_data(structured_data: StructuredData) -> UnstructuredData:
-    from subsurface.modules.visualization import to_pyvista_grid
-
-    sg = StructuredGrid(structured_data)
-    s = to_pyvista_grid(sg, data_order='C', data_set_name='topography')
-    un_s = s.cast_to_unstructured_grid()
-    un_s.triangulate(inplace=True)
-    vertex = un_s.points
-    cells = un_s.cells.reshape(-1, 4)[:, 1:]
-
-    unstructured_data = UnstructuredData.from_array(vertex, cells)
-    return unstructured_data
-
-
-def _get_raster_window(crop_to_extent, dataset):
-    from rasterio.windows import Window
-    # TODO: Add None check
-    # Get the indices of the window
-    left, bottom, right, top = crop_to_extent
-    row_start, col_start = dataset.index(left, top)
-    row_stop, col_stop = dataset.index(right, bottom)
-    # Read the data in the window
-    window = Window.from_slices((row_start, row_stop), (col_start, col_stop))
-    return window
+from typing import Sequence, Optional
+
+import numpy as np
+
+from ....core.structs.structured_elements.structured_grid import StructuredGrid
+from ....optional_requirements import require_rasterio
+from ....core.structs import StructuredData, UnstructuredData
+from ....core.utils.utils_core import get_extension
+from ....core.reader_helpers.readers_data import GenericReaderFilesHelper
+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:
+    rasterio = require_rasterio()
+
+    extension = get_extension(path)
+    if extension == '.tif':
+        structured_data = rasterio_dataset_to_structured_data(
+            dataset=rasterio.open(path),
+            crop_to_extent=crop_to_extent
+        )
+    else:
+        raise NotImplementedError('The extension given cannot be read yet')
+
+    return structured_data
+
+
+def read_structured_topography_to_unstructured(path) -> UnstructuredData:
+    structured_data = read_structured_topography(path)
+    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: 
+        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
+    
+    # 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]
+        )
+    }
+    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:
+    """For example, a dxf file"""
+    
+    additional_reader_kwargs = additional_reader_kwargs or {}
+    helper = GenericReaderFilesHelper(
+        file_or_buffer=path,
+        additional_reader_kwargs=additional_reader_kwargs or {}
+    )
+    unstructured_helper = ReaderUnstructuredHelper(helper)
+    unstruct: UnstructuredData = read_2d_mesh_to_unstruct(unstructured_helper)
+    return unstruct
+
+
+def topography_to_unstructured_data(structured_data: StructuredData) -> UnstructuredData:
+    from subsurface.modules.visualization import to_pyvista_grid
+
+    sg = StructuredGrid(structured_data)
+    s = to_pyvista_grid(sg, data_order='C', data_set_name='topography')
+    un_s = s.cast_to_unstructured_grid()
+    un_s.triangulate(inplace=True)
+    vertex = un_s.points
+    cells = un_s.cells.reshape(-1, 4)[:, 1:]
+
+    unstructured_data = UnstructuredData.from_array(vertex, cells)
+    return unstructured_data
+
+
+def _get_raster_window(crop_to_extent, dataset):
+    from rasterio.windows import Window
+    # TODO: Add None check
+    # Get the indices of the window
+    left, bottom, right, top = crop_to_extent
+    row_start, col_start = dataset.index(left, top)
+    row_stop, col_stop = dataset.index(right, bottom)
+    # Read the data in the window
+    window = Window.from_slices((row_start, row_stop), (col_start, col_stop))
+    return window