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

subsurface/core/utils/utils_core.py

@@ -1,38 +1,38 @@
-from typing import Union
-
-from pathlib import Path
-
-from ..structs import StructuredData, UnstructuredData
-
-
-def get_extension(path):
-    try:
-        p = Path(path)
-        return p.suffix
-    except TypeError:
-        return False
-
-
-def replace_outliers(base_data: Union[StructuredData, UnstructuredData], dim=0, perc=0.99, replace_for=None):
-    """@Edoardo Guerreiro https://stackoverflow.com/questions/60816533/
-     is-there-a-built-in-function-in-xarray-to-remove-outliers-from-a-dataset"""
-
-    data = base_data.data
-    # calculate percentile
-    threshold = data[dim].quantile(perc)
-
-    # find outliers and replace them with max among remaining values
-    mask = data[dim].where(abs(data[dim]) <= threshold)
-    if replace_for == 'max':
-        max_value = mask.max().values
-        # .where replace outliers with nan
-        mask = mask.fillna(max_value)
-    elif replace_for == 'min':
-        min_value = mask.min().values
-        # .where replace outliers with nan
-        mask = mask.fillna(min_value)
-
-    print(mask)
-    data[dim] = mask
-
-    return data
+from typing import Union
+
+from pathlib import Path
+
+from ..structs import StructuredData, UnstructuredData
+
+
+def get_extension(path):
+    try:
+        p = Path(path)
+        return p.suffix
+    except TypeError:
+        return False
+
+
+def replace_outliers(base_data: Union[StructuredData, UnstructuredData], dim=0, perc=0.99, replace_for=None):
+    """@Edoardo Guerreiro https://stackoverflow.com/questions/60816533/
+     is-there-a-built-in-function-in-xarray-to-remove-outliers-from-a-dataset"""
+
+    data = base_data.data
+    # calculate percentile
+    threshold = data[dim].quantile(perc)
+
+    # find outliers and replace them with max among remaining values
+    mask = data[dim].where(abs(data[dim]) <= threshold)
+    if replace_for == 'max':
+        max_value = mask.max().values
+        # .where replace outliers with nan
+        mask = mask.fillna(max_value)
+    elif replace_for == 'min':
+        min_value = mask.min().values
+        # .where replace outliers with nan
+        mask = mask.fillna(min_value)
+
+    print(mask)
+    data[dim] = mask
+
+    return data

subsurface/modules/reader/__init__.py

@@ -1,13 +1,13 @@
-# import warnings
-
-from .profiles import *
-
-from .topography.topo_core import read_structured_topography, read_unstructured_topography
-
-from .mesh.omf_mesh_reader import omf_stream_to_unstructs
-from .mesh.dxf_reader import dxf_stream_to_unstruct_input, dxf_file_to_unstruct_input
-from .mesh.mx_reader import mx_to_unstruc_from_binary
-from .mesh.obj_reader import load_obj_with_trimesh, load_obj_with_trimesh_from_binary
-from .mesh.glb_reader import load_gltf_with_trimesh
-
-from .volume.read_grav3d import read_msh_structured_grid
+# import warnings
+
+from .profiles import *
+
+from .topography.topo_core import read_structured_topography, read_unstructured_topography
+
+from .mesh.omf_mesh_reader import omf_stream_to_unstructs
+from .mesh.dxf_reader import dxf_stream_to_unstruct_input, dxf_file_to_unstruct_input
+from .mesh.mx_reader import mx_to_unstruc_from_binary
+from .mesh.obj_reader import load_obj_with_trimesh, load_obj_with_trimesh_from_binary
+from .mesh.glb_reader import load_gltf_with_trimesh
+
+from .volume.read_grav3d import read_msh_structured_grid

subsurface/modules/reader/faults/faults.py

@@ -1,80 +1,80 @@
-"""
-TODO: This is legacy code waiting to be updated to the new ideas
-
-
-"""
-
-import pandas as pd
-
-
-__all__ = ['read_faultsticks_kingdom', 'read_faultsticks_charisma']
-
-
-def read_faultsticks_kingdom(fp: str, name=None):
-    """
-    Reads in Kingdom fault stick files (kingdom) exported from Petrel (tested
-    with Petrel 2017) and returns pandas DataFrame.
-
-    Args:
-        fp (str): Filepath.
-        name (str, optional): Default: None.
-
-    Returns:
-        (pandas.DataFrame) Fault stick information stored in dataframe with
-        ["X", "Y", "Z", "formation", "stick id"] columns.
-
-    """
-    storage = []
-    with open(fp, "r") as file:
-        lines = file.readlines()
-        for line in lines:
-            line = line.split(" ")
-            X = float(line[6])
-            Y = float(line[7])
-            Z = float(line[9])
-            if name is None:
-                name = line[10]
-            else:
-                name = name
-            stick = int(line[-2])
-            storage.append([X, Y, Z, name, stick])
-
-    df = pd.DataFrame(storage)
-    df.columns = ["X", "Y", "Z", "name", "stick id"]
-    return df
-
-
-def read_faultsticks_charisma(fp:str, name=None):
-    """
-    Reads in charisma fault stick files exported from Petrel (tested with
-    Petrel 2017) and returns pandas DataFrame.
-
-    Args:
-        fp (str): Filepath.
-        name (str, optional): Default: None.
-
-    Returns:
-        (pandas.DataFrame) Fault stick information stored in dataframe with
-        ["X", "Y", "Z", "formation", "stick id"] columns.
-
-    """
-    storage = []
-    with open(fp, "r") as file:  # due to the variable delimiter length its
-                                 # easier to just manually read this in
-        lines = file.readlines()
-        for line in lines:
-            line = line.split(" ")
-            line = [l for l in line if len(l) >= 1]
-            X = float(line[3])
-            Y = float(line[4])
-            Z = float(line[5])
-            if name is None:
-                name = line[6]
-            else:
-                name = name
-            stick = int(line[-1])
-            storage.append([X, Y, Z, name, stick])
-
-    df = pd.DataFrame(storage)
-    df.columns = ["X", "Y", "Z", "name", "stick id"]
-    return df
+"""
+TODO: This is legacy code waiting to be updated to the new ideas
+
+
+"""
+
+import pandas as pd
+
+
+__all__ = ['read_faultsticks_kingdom', 'read_faultsticks_charisma']
+
+
+def read_faultsticks_kingdom(fp: str, name=None):
+    """
+    Reads in Kingdom fault stick files (kingdom) exported from Petrel (tested
+    with Petrel 2017) and returns pandas DataFrame.
+
+    Args:
+        fp (str): Filepath.
+        name (str, optional): Default: None.
+
+    Returns:
+        (pandas.DataFrame) Fault stick information stored in dataframe with
+        ["X", "Y", "Z", "formation", "stick id"] columns.
+
+    """
+    storage = []
+    with open(fp, "r") as file:
+        lines = file.readlines()
+        for line in lines:
+            line = line.split(" ")
+            X = float(line[6])
+            Y = float(line[7])
+            Z = float(line[9])
+            if name is None:
+                name = line[10]
+            else:
+                name = name
+            stick = int(line[-2])
+            storage.append([X, Y, Z, name, stick])
+
+    df = pd.DataFrame(storage)
+    df.columns = ["X", "Y", "Z", "name", "stick id"]
+    return df
+
+
+def read_faultsticks_charisma(fp:str, name=None):
+    """
+    Reads in charisma fault stick files exported from Petrel (tested with
+    Petrel 2017) and returns pandas DataFrame.
+
+    Args:
+        fp (str): Filepath.
+        name (str, optional): Default: None.
+
+    Returns:
+        (pandas.DataFrame) Fault stick information stored in dataframe with
+        ["X", "Y", "Z", "formation", "stick id"] columns.
+
+    """
+    storage = []
+    with open(fp, "r") as file:  # due to the variable delimiter length its
+                                 # easier to just manually read this in
+        lines = file.readlines()
+        for line in lines:
+            line = line.split(" ")
+            line = [l for l in line if len(l) >= 1]
+            X = float(line[3])
+            Y = float(line[4])
+            Z = float(line[5])
+            if name is None:
+                name = line[6]
+            else:
+                name = name
+            stick = int(line[-1])
+            storage.append([X, Y, Z, name, stick])
+
+    df = pd.DataFrame(storage)
+    df.columns = ["X", "Y", "Z", "name", "stick id"]
+    return df

subsurface/modules/reader/from_binary.py

@@ -1,46 +1,46 @@
-import json
-
-import numpy as np
-import xarray as xr
-
-
-def read_data(json_file_path, binary_file_path):
-    header = _read_json_header(json_file_path)
-    data_dict = _read_binary_data(binary_file_path, header)
-    return data_dict, header
-
-
-def _read_json_header(json_file_path):
-    with open(json_file_path, 'r') as f:
-        header = json.load(f)
-    return header
-
-
-def _read_binary_data(binary_file_path, header, order='F'):
-    # Initialize offset to 0
-    offset = 0
-    # Create a dictionary to hold the arrays
-    data_dict = {}
-
-    # Loop over the arrays
-    for array_name in ['vertex', 'cell', 'cell_attr', 'vertex_attr']:
-        # Get the shape and type of the array from the header
-        array_shape = header.get(f'{array_name}_shape')
-        array_type = header.get(f'{array_name}_types', 'float32')  # default to float32 if not found
-
-        # Calculate the number of elements in the array
-        num_elements = np.prod(array_shape)
-
-        # Read the data
-        data = np.fromfile(binary_file_path, dtype="int32", count=num_elements, offset=offset)
-        data = data.reshape(array_shape, order=order)
-
-        # Store the data in the dictionary
-        data_dict[array_name] = data
-
-        # Update the offset
-        offset += data.nbytes
-
-    return data_dict
-
-
+import json
+
+import numpy as np
+import xarray as xr
+
+
+def read_data(json_file_path, binary_file_path):
+    header = _read_json_header(json_file_path)
+    data_dict = _read_binary_data(binary_file_path, header)
+    return data_dict, header
+
+
+def _read_json_header(json_file_path):
+    with open(json_file_path, 'r') as f:
+        header = json.load(f)
+    return header
+
+
+def _read_binary_data(binary_file_path, header, order='F'):
+    # Initialize offset to 0
+    offset = 0
+    # Create a dictionary to hold the arrays
+    data_dict = {}
+
+    # Loop over the arrays
+    for array_name in ['vertex', 'cell', 'cell_attr', 'vertex_attr']:
+        # Get the shape and type of the array from the header
+        array_shape = header.get(f'{array_name}_shape')
+        array_type = header.get(f'{array_name}_types', 'float32')  # default to float32 if not found
+
+        # Calculate the number of elements in the array
+        num_elements = np.prod(array_shape)
+
+        # Read the data
+        data = np.fromfile(binary_file_path, dtype="int32", count=num_elements, offset=offset)
+        data = data.reshape(array_shape, order=order)
+
+        # Store the data in the dictionary
+        data_dict[array_name] = data
+
+        # Update the offset
+        offset += data.nbytes
+
+    return data_dict
+
+

subsurface/modules/reader/mesh/_GOCAD_mesh.py

@@ -1,82 +1,82 @@
-from dataclasses import dataclass, field
-
-import numpy as np
-
-
-@dataclass
-class GOCADMesh:
-    header: dict = field(default_factory=dict)
-    coordinate_system: dict = field(default_factory=dict)
-    property_class_headers: list = field(default_factory=list)
-    vertices: np.ndarray = field(default_factory=lambda: np.empty((0, 3)))
-    vertex_indices: np.ndarray = field(default_factory=lambda: np.array([]))
-    edges: np.ndarray = field(default_factory=lambda: np.empty((0, 3), dtype=int))
-    bstones: list = field(default_factory=list)
-    borders: list = field(default_factory=list)
-    metadata: dict = field(default_factory=dict)
-
-    @property
-    def vectorized_edges(self):
-        # Create index mapping from original to zero-based indices
-        idx_map = {old_idx: new_idx for new_idx, old_idx in enumerate(self.vertex_indices)}
-        # Map triangle indices
-        try:
-            triangles_mapped = np.vectorize(idx_map.get)(self.edges)
-        except TypeError as e:
-            self._verbose_debugging()
-            raise f"Error mapping indices for mesh: {e}"
-
-        return triangles_mapped
-
-    @property
-    def color(self):
-        """Try to get the color from the metadata. Can be in the form of:
-        *solid*color: #87ceeb or *solid*color: 0 0 1 1 (rgba).
-        Returns a color in the format acceptable by PyVista.
-        """
-        color = None
-
-        # First try to find a color value from the header
-        for key, value in self.header.items():
-            if 'color' in key.lower():
-                color = value.strip()
-                break
-
-        # If no color was found, return None
-        if not color:
-            return None
-
-        # Handle hexadecimal color string (e.g., #87ceeb)
-        if color.startswith('#') and len(color) == 7:
-            return color  # already valid as a hex string
-
-        # Handle space-separated RGBA or RGB values (e.g., "0 0 1 1")
-        if ' ' in color:
-            color_vals = [float(c) for c in color.split()]
-            if len(color_vals) == 4:  # RGBA
-                return color_vals[:3]  # ignore the alpha channel for now, as PyVista handles RGB
-            elif len(color_vals) == 3:  # RGB
-                return color_vals  # already in the right format
-
-        # Fallback: if none of the formats match, return None
-        return None
-
-    def _verbose_debugging(self):
-        # Create index mapping from original to zero-based indices
-        idx_map = {old_idx: new_idx for new_idx, old_idx in enumerate(self.vertex_indices)}
-
-        # Check for missing indices
-        unique_edge_indices = np.unique(self.edges)
-        missing_indices = set(unique_edge_indices) - set(idx_map.keys())
-        if missing_indices:
-            raise ValueError(f"Edges contain indices not found in vertex_indices: {missing_indices}")
-
-        # Map triangle indices using a list comprehension
-        try:
-            edges_flat = self.edges.flatten()
-            mapped_flat = [idx_map[idx] for idx in edges_flat]
-            triangles_mapped = np.array(mapped_flat).reshape(self.edges.shape)
-        except Exception as e:
-            raise Exception(f"Error mapping indices for mesh: {e}")
-
-        return triangles_mapped
+from dataclasses import dataclass, field
+
+import numpy as np
+
+
+@dataclass
+class GOCADMesh:
+    header: dict = field(default_factory=dict)
+    coordinate_system: dict = field(default_factory=dict)
+    property_class_headers: list = field(default_factory=list)
+    vertices: np.ndarray = field(default_factory=lambda: np.empty((0, 3)))
+    vertex_indices: np.ndarray = field(default_factory=lambda: np.array([]))
+    edges: np.ndarray = field(default_factory=lambda: np.empty((0, 3), dtype=int))
+    bstones: list = field(default_factory=list)
+    borders: list = field(default_factory=list)
+    metadata: dict = field(default_factory=dict)
+
+    @property
+    def vectorized_edges(self):
+        # Create index mapping from original to zero-based indices
+        idx_map = {old_idx: new_idx for new_idx, old_idx in enumerate(self.vertex_indices)}
+        # Map triangle indices
+        try:
+            triangles_mapped = np.vectorize(idx_map.get)(self.edges)
+        except TypeError as e:
+            self._verbose_debugging()
+            raise f"Error mapping indices for mesh: {e}"
+
+        return triangles_mapped
+
+    @property
+    def color(self):
+        """Try to get the color from the metadata. Can be in the form of:
+        *solid*color: #87ceeb or *solid*color: 0 0 1 1 (rgba).
+        Returns a color in the format acceptable by PyVista.
+        """
+        color = None
+
+        # First try to find a color value from the header
+        for key, value in self.header.items():
+            if 'color' in key.lower():
+                color = value.strip()
+                break
+
+        # If no color was found, return None
+        if not color:
+            return None
+
+        # Handle hexadecimal color string (e.g., #87ceeb)
+        if color.startswith('#') and len(color) == 7:
+            return color  # already valid as a hex string
+
+        # Handle space-separated RGBA or RGB values (e.g., "0 0 1 1")
+        if ' ' in color:
+            color_vals = [float(c) for c in color.split()]
+            if len(color_vals) == 4:  # RGBA
+                return color_vals[:3]  # ignore the alpha channel for now, as PyVista handles RGB
+            elif len(color_vals) == 3:  # RGB
+                return color_vals  # already in the right format
+
+        # Fallback: if none of the formats match, return None
+        return None
+
+    def _verbose_debugging(self):
+        # Create index mapping from original to zero-based indices
+        idx_map = {old_idx: new_idx for new_idx, old_idx in enumerate(self.vertex_indices)}
+
+        # Check for missing indices
+        unique_edge_indices = np.unique(self.edges)
+        missing_indices = set(unique_edge_indices) - set(idx_map.keys())
+        if missing_indices:
+            raise ValueError(f"Edges contain indices not found in vertex_indices: {missing_indices}")
+
+        # Map triangle indices using a list comprehension
+        try:
+            edges_flat = self.edges.flatten()
+            mapped_flat = [idx_map[idx] for idx in edges_flat]
+            triangles_mapped = np.array(mapped_flat).reshape(self.edges.shape)
+        except Exception as e:
+            raise Exception(f"Error mapping indices for mesh: {e}")
+
+        return triangles_mapped