subsurface-terra 2025.1.0rc8__tar.gz → 2025.1.0rc11__tar.gz

subsurface_terra-2025.1.0rc11/.teamcity/Subsurface/buildTypes/Subsurface_ReleaseSubsurface.xml

@@ -0,0 +1,60 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<template xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" uuid="671f325d-03f3-4855-994a-eb6080da9084" xsi:noNamespaceSchemaLocation="https://www.jetbrains.com/teamcity/schemas/2021.1/project-config.xsd">
+  <name>Release Subsurface</name>
+  <settings>
+    <parameters>
+      <param name="env.PACKAGE_VERSION" value="" spec="text description='The version that I want to release' label='Package version' validationMode='any' display='prompt'" />
+      <param name="env.TWINE_PASSWORD" value="credentialsJSON:e9a0b402-f8b3-4f86-978c-9c88c456dc9c" spec="password display='normal'" />
+    </parameters>
+    <build-runners>
+      <runner id="Git_Tagging" name="Git Tagging" type="simpleRunner">
+        <parameters>
+          <param name="script.content"><![CDATA[git tag v%env.PACKAGE_VERSION%
+git push origin v%env.PACKAGE_VERSION%]]></param>
+          <param name="teamcity.step.mode" value="default" />
+          <param name="use.custom.script" value="true" />
+        </parameters>
+      </runner>
+      <runner id="Build" name="Build" type="simpleRunner">
+        <parameters>
+          <param name="script.content"><![CDATA[python -m pip install --upgrade build
+python -m build]]></param>
+          <param name="teamcity.kubernetes.executor.pull.policy" value="IfNotPresent" />
+          <param name="teamcity.step.mode" value="default" />
+          <param name="use.custom.script" value="true" />
+        </parameters>
+      </runner>
+      <runner id="Push_to_PyPi" name="Push to PyPi" type="simpleRunner">
+        <parameters>
+          <param name="script.content"><![CDATA[python -m pip install --upgrade twine
+python -m twine upload dist/* -u __token__ -p %env.TWINE_PASSWORD%]]></param>
+          <param name="teamcity.kubernetes.executor.pull.policy" value="IfNotPresent" />
+          <param name="teamcity.step.mode" value="default" />
+          <param name="use.custom.script" value="true" />
+        </parameters>
+      </runner>
+      <runner id="Push_To_GitHub" name="Push To GitHub" type="simpleRunner">
+        <parameters>
+          <param name="script.content" value="gh release create %env.PACKAGE_VERSION% dist/* --title &quot;%env.PACKAGE_VERSION%&quot; --notes &quot;Release notes here&quot;" />
+          <param name="teamcity.kubernetes.executor.pull.policy" value="IfNotPresent" />
+          <param name="teamcity.step.mode" value="default" />
+          <param name="use.custom.script" value="true" />
+        </parameters>
+      </runner>
+    </build-runners>
+    <vcs-settings>
+      <vcs-entry-ref root-id="Subsurface_HttpsGithubComTerranigmaSolutionsSubsurfaceRefsHeadsMain" />
+    </vcs-settings>
+    <requirements />
+    <build-triggers />
+    <build-extensions>
+      <extension id="BUILD_EXT_1" type="perfmon">
+        <parameters>
+          <param name="teamcity.perfmon.feature.enabled" value="true" />
+        </parameters>
+      </extension>
+    </build-extensions>
+    <cleanup />
+  </settings>
+</template>
+

subsurface_terra-2025.1.0rc11/.teamcity/Subsurface/buildTypes/Subsurface_ReleaseSubsurface_2.xml

@@ -0,0 +1,37 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<build-type xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" uuid="c15fb876-7044-47cd-a3b0-676767e4ca63" xsi:noNamespaceSchemaLocation="https://www.jetbrains.com/teamcity/schemas/2021.1/project-config.xsd">
+  <name>Release Subsurface</name>
+  <description />
+  <settings ref="ReleasePythonPackage">
+    <parameters />
+    <build-runners order="Git_Tagging, Build, Push_to_PyPi, Push_To_GitHub">
+      <runner id="Build" name="Build" type="simpleRunner">
+        <parameters>
+          <param name="script.content"><![CDATA[echo Cleaning build artifacts...
+rmdir /s /q dist
+rmdir /s /q build
+echo Clean complete.
+
+python -m pip install --upgrade build
+python -m build]]></param>
+          <param name="teamcity.step.mode" value="default" />
+          <param name="use.custom.script" value="true" />
+        </parameters>
+      </runner>
+      <runner id="Push_To_GitHub" name="Push To GitHub" type="simpleRunner">
+        <parameters>
+          <param name="script.content" value="gh release create %env.PACKAGE_VERSION% dist/*  --notes &quot;Release notes here&quot; --repo terranigma-solutions/subsurface" />
+          <param name="teamcity.step.mode" value="default" />
+          <param name="use.custom.script" value="true" />
+        </parameters>
+      </runner>
+    </build-runners>
+    <vcs-settings>
+      <vcs-entry-ref root-id="Subsurface_HttpsGithubComTerranigmaSolutionsSubsurfaceRefsHeadsMain1" />
+    </vcs-settings>
+    <requirements />
+    <build-triggers />
+    <cleanup />
+  </settings>
+</build-type>
+

subsurface_terra-2025.1.0rc11/.teamcity/Subsurface/buildTypes/Subsurface_Testing.xml

@@ -0,0 +1,129 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<build-type xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" uuid="ed495f4f-4df2-4a37-bbfe-2489430a46e8" xsi:noNamespaceSchemaLocation="https://www.jetbrains.com/teamcity/schemas/2021.1/project-config.xsd">
+  <name>Testing</name>
+  <description />
+  <settings>
+    <parameters>
+      <param name="REQUIREMENT_LEVEL" value="READ_MESH" />
+      <param name="env.MPLBACKEND" value="Agg" />
+      <param name="env.PATH_TO_ASCII_DRILLHOLES" value="%env.TERRA_PATH_DEVOPS%/boreholes/ASCII_drillholes/" />
+      <param name="env.PATH_TO_BGR" value="%env.TERRA_PATH_DEVOPS%/boreholes/" />
+      <param name="env.PATH_TO_BOLIDEN" value="%env.TERRA_PATH_DEVOPS%/combined/Leapfrog_OMF/Garpenberg_global_20220715.omf" />
+      <param name="env.PATH_TO_GLB" value="%env.TERRA_PATH_DEVOPS%/meshes/GLB - GLTF/Duck.glb" />
+      <param name="env.PATH_TO_GLB_COMPLEX" value="%env.TERRA_PATH_DEVOPS%/meshes/GLB - GLTF/GlbFile.glb" />
+      <param name="env.PATH_TO_INTERPRETATION" value="%env.TERRA_PATH_DEVOPS%/meshes/Seismic/Anl2-1.tif" />
+      <param name="env.PATH_TO_MAGNETIC_INTERPRETATION" value="%env.TERRA_PATH_DEVOPS%/meshes/Magnetic/Plate 2a - Profile 1 2D inversion.pdf" />
+      <param name="env.PATH_TO_MTL" value="%env.TERRA_PATH_DEVOPS%/meshes/OBJ/Broadhaven_Obj/model/model.mtl" />
+      <param name="env.PATH_TO_OBJ" value="%env.TERRA_PATH_DEVOPS%/meshes/OBJ/Broadhaven_Obj/model/model.obj" />
+      <param name="env.PATH_TO_OBJ_FACE_I" value="%env.TERRA_PATH_DEVOPS%/meshes/OBJ/Faces/face1.obj" />
+      <param name="env.PATH_TO_OBJ_FACE_II" value="%env.TERRA_PATH_DEVOPS%/meshes/OBJ/Faces/Lapp_458_Rum_19_2_2024-02-21_0820_scan5_geoim4.obj" />
+      <param name="env.PATH_TO_OBJ_GALLERIES_I" value="%env.TERRA_PATH_DEVOPS%/meshes/OBJ/Galleries/Solid1.obj" />
+      <param name="env.PATH_TO_OBJ_MULTIMATERIAL_II" value="%env.TERRA_PATH_DEVOPS%/meshes/OBJ/MultiMaterialObj/MultiMaterialObj.obj" />
+      <param name="env.PATH_TO_OBJ_SCANS" value="%env.TERRA_PATH_DEVOPS%/meshes/OBJ/Core scans Boliden/rsrbF9l2zc/model.obj" />
+      <param name="env.PATH_TO_OMF" value="%env.TERRA_PATH_DEVOPS%/combined/Leapfrog_OMF/Collinstown.omf" />
+      <param name="env.PATH_TO_SECTION" value="%env.TERRA_PATH_DEVOPS%/meshes/Seismic/L1_CDP-Coords.txt" />
+      <param name="env.PATH_TO_SEISMIC" value="%env.TERRA_PATH_DEVOPS%/meshes/Seismic/Linie01.segy" />
+      <param name="env.PATH_TO_SEISMIC_FINAL" value="%env.TERRA_PATH_DEVOPS%/meshes/Seismic/L1_final-mig.sgy" />
+      <param name="env.PATH_TO_SPREMBERG_ASSAY" value="%env.TERRA_PATH_DEVOPS%/boreholes/Spremberg/Spremberg_assay.csv" />
+      <param name="env.PATH_TO_SPREMBERG_COLLAR" value="%env.TERRA_PATH_DEVOPS%/boreholes/Spremberg/Spremberg_collar_updated.csv" />
+      <param name="env.PATH_TO_SPREMBERG_STRATIGRAPHY" value="%env.TERRA_PATH_DEVOPS%/boreholes/Spremberg/Spremberg_stratigraphy.csv" />
+      <param name="env.PATH_TO_SPREMBERG_SURVEY" value="%env.TERRA_PATH_DEVOPS%/boreholes/Spremberg/Spremberg_survey.csv" />
+      <param name="env.PATH_TO_WEISWEILER" value="%env.TERRA_PATH_DEVOPS%/meshes/Weisweiler/" />
+      <param name="env.TERRA_PATH_DEVOPS" value="D:\OneDrive - Terranigma Solutions GmbH/Documents - Terranigma Base/DevOps/SubsurfaceTestData/" />
+    </parameters>
+    <build-runners>
+      <runner id="Setup" name="Setup" type="simpleRunner">
+        <parameters>
+          <param name="script.content"><![CDATA[@echo on
+python -m venv venv
+call venv\Scripts\activate
+venv\Scripts\python -m pip install --upgrade pip
+
+echo Checking directory...
+dir
+dir .requirements
+
+venv\Scripts\pip install --verbose -r requirements/requirements_dev.txt
+venv\Scripts\pip install --verbose teamcity-messages]]></param>
+          <param name="teamcity.step.mode" value="default" />
+          <param name="use.custom.script" value="true" />
+        </parameters>
+      </runner>
+      <runner id="Run_Test" name="Run Test: Core" type="simpleRunner">
+        <parameters>
+          <param name="script.content"><![CDATA[venv\Scripts\pip install --verbose -r requirements/requirements_plot.txt
+
+@echo on
+set REQUIREMENT_LEVEL=READ_MESH
+echo REQUIREMENT_LEVEL is %REQUIREMENT_LEVEL%
+venv\Scripts\python -m pytest --teamcity -v -m core]]></param>
+          <param name="teamcity.step.mode" value="default" />
+          <param name="use.custom.script" value="true" />
+        </parameters>
+      </runner>
+      <runner id="Run_Test_2" name="Run Test: Mesh" type="simpleRunner">
+        <parameters>
+          <param name="script.content"><![CDATA[venv\Scripts\pip install --verbose -r requirements/requirements_mesh.txt
+
+@echo on
+set REQUIREMENT_LEVEL=READ_MESH
+echo REQUIREMENT_LEVEL is %REQUIREMENT_LEVEL%
+venv\Scripts\python -m pytest --teamcity -v]]></param>
+          <param name="teamcity.step.mode" value="execute_if_failed" />
+          <param name="use.custom.script" value="true" />
+        </parameters>
+      </runner>
+      <runner id="Run_Test_wells" name="Run Test: Wells" type="simpleRunner">
+        <parameters>
+          <param name="script.content"><![CDATA[venv\Scripts\pip install --verbose -r requirements/requirements_wells.txt
+
+@echo on
+set REQUIREMENT_LEVEL=READ_WELL
+echo REQUIREMENT_LEVEL is %REQUIREMENT_LEVEL%
+venv\Scripts\python -m pytest --teamcity -v]]></param>
+          <param name="teamcity.step.mode" value="execute_if_failed" />
+          <param name="use.custom.script" value="true" />
+        </parameters>
+      </runner>
+    </build-runners>
+    <vcs-settings>
+      <vcs-entry-ref root-id="Subsurface_HttpsGithubComTerranigmaSolutionsSubsurfaceRefsHeadsMain2" />
+    </vcs-settings>
+    <requirements />
+    <build-triggers>
+      <build-trigger id="TRIGGER_4" type="vcsTrigger">
+        <parameters>
+          <param name="branchFilter"><![CDATA[+pr:draft=false
++:refs/heads/main]]></param>
+          <param name="enableQueueOptimization" value="true" />
+          <param name="quietPeriodMode" value="DO_NOT_USE" />
+        </parameters>
+      </build-trigger>
+    </build-triggers>
+    <build-extensions>
+      <extension id="perfmon" type="perfmon">
+        <parameters>
+          <param name="teamcity.perfmon.feature.enabled" value="true" />
+        </parameters>
+      </extension>
+      <extension id="BUILD_EXT_5" type="commit-status-publisher">
+        <parameters>
+          <param name="github_authentication_type" value="token" />
+          <param name="github_host" value="https://api.github.com" />
+          <param name="publisherId" value="githubStatusPublisher" />
+          <param name="secure:github_access_token" value="credentialsJSON:4df4bdb0-1278-4834-a702-18ae3a286003" />
+        </parameters>
+      </extension>
+      <extension id="BUILD_EXT_6" type="pullRequests">
+        <parameters>
+          <param name="authenticationType" value="token" />
+          <param name="filterAuthorRole" value="MEMBER" />
+          <param name="providerType" value="github" />
+          <param name="secure:accessToken" value="credentialsJSON:4df4bdb0-1278-4834-a702-18ae3a286003" />
+        </parameters>
+      </extension>
+    </build-extensions>
+    <cleanup />
+  </settings>
+</build-type>
+

subsurface_terra-2025.1.0rc11/.teamcity/Subsurface/project-config.xml

@@ -0,0 +1,19 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" uuid="02a92682-f6c2-4edf-af46-08d095b0ce77" xsi:noNamespaceSchemaLocation="https://www.jetbrains.com/teamcity/schemas/2021.1/project-config.xsd">
+  <name>Subsurface</name>
+  <parameters />
+  <project-extensions>
+    <extension id="PROJECT_EXT_15" type="versionedSettings">
+      <parameters>
+        <param name="buildSettings" value="ALWAYS_USE_CURRENT" />
+        <param name="credentialsStorageType" value="credentialsJSON" />
+        <param name="enabled" value="true" />
+        <param name="ignoreChangesInDependenciesAndVcsSettings" value="false" />
+        <param name="rootId" value="Subsurface_HttpsGithubComTerranigmaSolutionsSubsurfaceRefsHeadsMain" />
+        <param name="showChanges" value="false" />
+      </parameters>
+    </extension>
+  </project-extensions>
+  <cleanup />
+</project>
+

subsurface_terra-2025.1.0rc11/.teamcity/Subsurface/vcsRoots/Subsurface_HttpsGithubComTerranigmaSolutionsSubsurfaceRefsHeadsMain.xml

@@ -0,0 +1,17 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<vcs-root xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" uuid="b5c00aa4-356b-4c94-8113-009cde53f17b" type="jetbrains.git" xsi:noNamespaceSchemaLocation="https://www.jetbrains.com/teamcity/schemas/2021.1/project-config.xsd">
+  <name>https://github.com/terranigma-solutions/subsurface#refs/heads/main</name>
+  <param name="agentCleanFilesPolicy" value="ALL_UNTRACKED" />
+  <param name="agentCleanPolicy" value="ON_BRANCH_CHANGE" />
+  <param name="authMethod" value="PASSWORD" />
+  <param name="branch" value="refs/heads/main" />
+  <param name="ignoreKnownHosts" value="true" />
+  <param name="secure:password" value="credentialsJSON:4df4bdb0-1278-4834-a702-18ae3a286003" />
+  <param name="submoduleCheckout" value="CHECKOUT" />
+  <param name="teamcity:branchSpec" value="refs/heads/*" />
+  <param name="url" value="https://github.com/terranigma-solutions/subsurface" />
+  <param name="useAlternates" value="AUTO" />
+  <param name="username" value="Leguark" />
+  <param name="usernameStyle" value="USERID" />
+</vcs-root>
+

subsurface_terra-2025.1.0rc11/.teamcity/Subsurface/vcsRoots/Subsurface_HttpsGithubComTerranigmaSolutionsSubsurfaceRefsHeadsMain1.xml

@@ -0,0 +1,16 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<vcs-root xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" uuid="e9cb014a-3f5f-4e33-8d40-9c5cb180a9d6" type="jetbrains.git" xsi:noNamespaceSchemaLocation="https://www.jetbrains.com/teamcity/schemas/2021.1/project-config.xsd">
+  <name>https://github.com/terranigma-solutions/subsurface#refs/heads/main (1)</name>
+  <param name="agentCleanFilesPolicy" value="ALL_UNTRACKED" />
+  <param name="agentCleanPolicy" value="ON_BRANCH_CHANGE" />
+  <param name="authMethod" value="PASSWORD" />
+  <param name="branch" value="refs/heads/main" />
+  <param name="ignoreKnownHosts" value="true" />
+  <param name="secure:password" value="credentialsJSON:4df4bdb0-1278-4834-a702-18ae3a286003" />
+  <param name="submoduleCheckout" value="CHECKOUT" />
+  <param name="url" value="https://github.com/terranigma-solutions/subsurface" />
+  <param name="useAlternates" value="AUTO" />
+  <param name="username" value="Leguark" />
+  <param name="usernameStyle" value="USERID" />
+</vcs-root>
+

subsurface_terra-2025.1.0rc11/.teamcity/Subsurface/vcsRoots/Subsurface_HttpsGithubComTerranigmaSolutionsSubsurfaceRefsHeadsMain2.xml

@@ -0,0 +1,16 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<vcs-root xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" uuid="a5d752d7-0d2a-4197-b779-2049040d97ba" type="jetbrains.git" xsi:noNamespaceSchemaLocation="https://www.jetbrains.com/teamcity/schemas/2021.1/project-config.xsd">
+  <name>https://github.com/terranigma-solutions/subsurface#refs/heads/main (2)</name>
+  <param name="agentCleanFilesPolicy" value="ALL_UNTRACKED" />
+  <param name="agentCleanPolicy" value="ON_BRANCH_CHANGE" />
+  <param name="authMethod" value="PASSWORD" />
+  <param name="branch" value="refs/heads/main" />
+  <param name="ignoreKnownHosts" value="true" />
+  <param name="secure:password" value="credentialsJSON:4df4bdb0-1278-4834-a702-18ae3a286003" />
+  <param name="submoduleCheckout" value="CHECKOUT" />
+  <param name="url" value="https://github.com/terranigma-solutions/subsurface" />
+  <param name="useAlternates" value="AUTO" />
+  <param name="username" value="Leguark" />
+  <param name="usernameStyle" value="USERID" />
+</vcs-root>
+

{subsurface_terra-2025.1.0rc8/subsurface_terra.egg-info → subsurface_terra-2025.1.0rc11}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: subsurface_terra
-Version: 2025.1.0rc8
+Version: 2025.1.0rc11
 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-2025.1.0rc8 → subsurface_terra-2025.1.0rc11}/requirements/requirements_wells.txt

@@ -1,3 +1,4 @@
 openpyxl
 wellpathpy
+scipy
 

{subsurface_terra-2025.1.0rc8 → subsurface_terra-2025.1.0rc11}/subsurface/_version.py

@@ -17,5 +17,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '2025.1.0rc8'
+__version__ = version = '2025.1.0rc11'
 __version_tuple__ = version_tuple = (2025, 1, 0)

{subsurface_terra-2025.1.0rc8 → subsurface_terra-2025.1.0rc11}/subsurface/core/geological_formats/boreholes/survey.py

@@ -111,9 +111,11 @@ def _map_attrs_to_measured_depths(attrs: pd.DataFrame, survey: Survey) -> pd.Dat
 
     # Start with a copy of the existing attributes DataFrame
     new_attrs = survey.survey_trajectory.data.points_attributes.copy()
-    if 'component lith' in attrs.columns:
+    if 'component lith' in attrs.columns and 'lith_ids' not in attrs.columns:
         # Factorize lith components directly in-place
         attrs['lith_ids'], _ = pd.factorize(attrs['component lith'], use_na_sentinel=True)
+    else:
+        pass
 
     # Add missing columns from attrs, preserving their dtypes
     for col in attrs.columns.difference(new_attrs.columns):
@@ -152,7 +154,7 @@ def _map_attrs_to_measured_depths(attrs: pd.DataFrame, survey: Survey) -> pd.Dat
                 continue
             attr_to_interpolate = attrs_well[col]
             # make sure the attr_to_interpolate is not a string
-            if attr_to_interpolate.dtype == 'O':
+            if attr_to_interpolate.dtype == 'O' or isinstance(attr_to_interpolate.dtype, pd.CategoricalDtype): 
                 continue
             if col in ['lith_ids', 'component lith']:
                 interp_kind = 'nearest'

{subsurface_terra-2025.1.0rc8 → subsurface_terra-2025.1.0rc11}/subsurface/modules/reader/mesh/_trimesh_reader.py

@@ -37,9 +37,9 @@ def load_with_trimesh(path_to_file_or_buffer, file_type: Optional[str] = None,
             # Old Z axis → New -Y axis
             # Old X axis → Remains as X axis
             transform = np.array([
-                    [1, 0, 0, 0],  # X → X
-                    [0, 0, 1, 0],  # Y → Z 
-                    [0, 1, 0, 0],  # Z → -Y
+                    [1, 0, 0, 0],  
+                    [0, 0, -1, 0],  
+                    [0, 1, 0, 0], 
                     [0, 0, 0, 1]
             ])
 

{subsurface_terra-2025.1.0rc8 → subsurface_terra-2025.1.0rc11}/subsurface/modules/reader/mesh/mx_reader.py

@@ -157,7 +157,7 @@ def _process_mesh(mesh_lines) -> Optional[GOCADMesh]:
             continue
 
         if in_tface:
-            if line.startswith('VRTX'):
+            if line.startswith('VRTX') or line.startswith('PVRTX'):
                 # Parse vertex line
                 parts = line.split()
                 if len(parts) >= 5:
@@ -167,6 +167,7 @@ def _process_mesh(mesh_lines) -> Optional[GOCADMesh]:
                     vertex_indices.append(vid)
                     vertex_list.append([x, y, z])
                     vid_to_index[vid] = len(vertex_list) - 1
+                    # If PVRTX then there could be more columns with property values. For now, we are just parsing the vertex coordinates.
                 continue
             elif line.startswith('ATOM'):
                 # Parse ATOM line

subsurface_terra-2025.1.0rc11/subsurface/modules/reader/volume/read_volume.py

@@ -0,0 +1,230 @@
+import os
+from io import BytesIO
+from typing import Union
+
+from subsurface.core.structs import StructuredData
+
+from .... import optional_requirements
+from ....core.structs import UnstructuredData
+from subsurface.core.reader_helpers.readers_data import GenericReaderFilesHelper
+import numpy as np
+import pandas as pd
+
+
+def read_VTK_structured_grid(file_or_buffer: Union[str, BytesIO], active_scalars: str) -> StructuredData:
+    pv = optional_requirements.require_pyvista()
+
+    if isinstance(file_or_buffer, BytesIO):
+        # If file_or_buffer is a BytesIO, write it to a temporary file
+        from tempfile import NamedTemporaryFile
+        with NamedTemporaryFile('wb', suffix='.vtk', delete=False) as temp_file:
+            # Write the BytesIO content to the temporary file
+            getvalue: bytes = file_or_buffer.getvalue()
+            temp_file.write(getvalue)
+            temp_file.flush()  # Make sure all data is written
+            temp_file_name = temp_file.name  # Store the temporary file name
+        try:
+            # Use pyvista.read() to read from the temporary file
+            pyvista_obj = pv.read(temp_file_name)
+        finally:
+            # Ensure the temporary file is deleted after reading
+            os.remove(temp_file_name)
+    else:
+        # If it's a file path, read directly
+        pyvista_obj = pv.read(file_or_buffer)
+    try:
+        pyvista_struct: pv.ExplicitStructuredGrid = pv_cast_to_explicit_structured_grid(pyvista_obj)
+    except Exception as e:
+        raise f"The file is not a structured grid: {e}"
+
+    if PLOT := False:
+        pyvista_struct.set_active_scalars(active_scalars)
+        pyvista_struct.plot()
+
+    struct: StructuredData = StructuredData.from_pyvista_structured_grid(
+        grid=pyvista_struct,
+        data_array_name=active_scalars
+    )
+
+    return struct
+
+
+def read_volumetric_mesh_to_subsurface(reader_helper_coord: GenericReaderFilesHelper,
+                                       reader_helper_attr: GenericReaderFilesHelper) -> UnstructuredData:
+    df_coord = read_volumetric_mesh_coord_file(reader_helper_coord)
+    if len(df_coord.columns) == 1:
+        raise ValueError(
+            "The attributes file has only one column, probably the columns are not being separated correctly. Use 'sep' in Additional Reader Arguments"
+        )
+
+    df_attr = read_volumetric_mesh_attr_file(reader_helper_attr)
+    # Check if there are more than one column and if it is only one raise an error that probably the columns have not been properly separated. Use "sep" in Additional Reader Arguments
+    if len(df_attr.columns) == 1:
+        raise ValueError(
+            "The attributes file has only one column, probably the columns are not being separated correctly. Use 'sep' in Additional Reader Arguments"
+        )
+    
+    combined_df = df_coord.merge(df_attr, left_index=True, right_index=True)
+    ud = UnstructuredData.from_array(
+        vertex=combined_df[['x', 'y', 'z']], cells="points",
+        attributes=combined_df[['pres', 'temp', 'sg', 'xco2']]
+    )
+    return ud
+
+
+def read_volumetric_mesh_coord_file(reader_helper: GenericReaderFilesHelper) -> pd.DataFrame:
+    df = pd.read_csv(
+        filepath_or_buffer=reader_helper.file_or_buffer,
+        **reader_helper.pandas_reader_kwargs
+    )
+    if reader_helper.columns_map is not None:
+        df.rename(
+            mapper=reader_helper.columns_map,
+            axis="columns",
+            inplace=True
+        )
+
+    df.dropna(axis=0, inplace=True)
+
+    df.x = df.x.astype(float)
+    df.y = df.y.astype(float)
+    df.z = df.z.astype(float)
+    # Throw error if empty
+    if df.empty:
+        raise ValueError("The file is empty")
+    
+    return df
+
+
+def read_volumetric_mesh_attr_file(reader_helper: GenericReaderFilesHelper) -> pd.DataFrame:
+    df = pd.read_table(reader_helper.file_or_buffer, **reader_helper.pandas_reader_kwargs)
+    df.columns = df.columns.astype(str).str.strip()
+    return df
+
+
+def pv_cast_to_explicit_structured_grid(pyvista_object: 'pv.DataSet') -> 'pv.ExplicitStructuredGrid':
+    pv = optional_requirements.require_pyvista()
+
+    match pyvista_object:
+        case pv.RectilinearGrid() as rectl_grid:
+            return __pv_convert_rectilinear_to_explicit(rectl_grid)
+        case pv.UnstructuredGrid() as unstr_grid:
+            return __pv_convert_unstructured_to_explicit(unstr_grid)
+        case _:
+            return pyvista_object.cast_to_explicit_structured_grid()
+
+
+def __pv_convert_unstructured_to_explicit(unstr_grid):
+    """
+    Convert a PyVista UnstructuredGrid to an ExplicitStructuredGrid if possible.
+    """
+    pv = optional_requirements.require_pyvista()
+
+    # First check if the grid has the necessary attributes to be treated as structured
+    if not hasattr(unstr_grid, 'n_cells') or unstr_grid.n_cells == 0:
+        raise ValueError("The unstructured grid has no cells.")
+    
+    # Try to detect if the grid has a structured topology
+    # Check if the grid has cell type 11 (VTK_VOXEL) or 12 (VTK_HEXAHEDRON)
+    cell_types = unstr_grid.celltypes
+    
+    # Voxels (11) and hexahedra (12) are the cell types used in structured grids
+    if not all(ct in [11, 12] for ct in cell_types):
+        raise ValueError("The unstructured grid contains non-hexahedral cells and cannot be converted to explicit structured.")
+    
+    # Try to infer dimensions from the grid
+    try:
+        # Method 1: Try PyVista's built-in conversion if available
+        return unstr_grid.cast_to_explicit_structured_grid()
+    except (AttributeError, TypeError):
+        pass
+    
+    try:
+        # Method 2: If the grid has dimensions stored as field data
+        if "dimensions" in unstr_grid.field_data:
+            dims = unstr_grid.field_data["dimensions"]
+            if len(dims) == 3:
+                nx, ny, nz = dims
+                # Verify that dimensions match the number of cells
+                if (nx-1)*(ny-1)*(nz-1) != unstr_grid.n_cells:
+                    raise ValueError("Stored dimensions do not match the number of cells.")
+                
+                # Extract points and reorder if needed
+                points = unstr_grid.points.reshape((nx, ny, nz, 3))
+                
+                # Create explicit structured grid
+                explicit_grid = pv.ExplicitStructuredGrid((nx, ny, nz), points.reshape((-1, 3)))
+                explicit_grid.compute_connectivity()
+                
+                # Transfer data arrays
+                for name, array in unstr_grid.cell_data.items():
+                    explicit_grid.cell_data[name] = array.copy()
+                for name, array in unstr_grid.point_data.items():
+                    explicit_grid.point_data[name] = array.copy()
+                for name, array in unstr_grid.field_data.items():
+                    if name != "dimensions":  # Skip dimensions field
+                        explicit_grid.field_data[name] = array.copy()
+                
+                return explicit_grid
+    except (ValueError, KeyError):
+        pass
+    
+    # If none of the above methods work, use PyVista's extract_cells function
+    # to reconstruct the structured grid if possible
+    try:
+        # This is a best-effort approach that tries multiple strategies
+        return pv.core.filters.convert_unstructured_to_structured_grid(unstr_grid)
+    except Exception as e:
+        raise ValueError(f"Failed to convert unstructured grid to explicit structured grid: {e}")
+    
+def __pv_convert_rectilinear_to_explicit(rectl_grid):
+
+    pv = optional_requirements.require_pyvista()
+
+    # Extract the coordinate arrays from the input RectilinearGrid.
+    x = np.asarray(rectl_grid.x)
+    y = np.asarray(rectl_grid.y)
+    z = np.asarray(rectl_grid.z)
+
+    # Helper function: "double" the coordinates to produce an expanded set
+    # that, when processed internally via np.unique, returns the original nodal values.
+    def doubled_coords(arr):
+        return np.repeat(arr, 2)[1:-1]
+
+    # Double the coordinate arrays.
+    xcorn = doubled_coords(x)
+    ycorn = doubled_coords(y)
+    zcorn = doubled_coords(z)
+
+    # Build a complete grid of corner points via meshgrid. Fortran ('F') order ensures
+    # the connectivity ordering aligns with VTK's expectations.
+    xx, yy, zz = np.meshgrid(xcorn, ycorn, zcorn, indexing='ij')
+    corners = np.column_stack((xx.ravel(order='F'),
+                               yy.ravel(order='F'),
+                               zz.ravel(order='F')))
+
+    # The dimensions to pass to the ExplicitStructuredGrid constructor should be
+    # the counts of unique coordinates in each direction.
+    dims = (len(np.unique(xcorn)),
+            len(np.unique(ycorn)),
+            len(np.unique(zcorn)))
+
+    # Create the ExplicitStructuredGrid.
+    explicit_grid = pv.ExplicitStructuredGrid(dims, corners)
+    explicit_grid.compute_connectivity()
+
+    # --- Copy associated data arrays ---
+
+    # Transfer all cell data arrays.
+    for name, array in rectl_grid.cell_data.items():
+        explicit_grid.cell_data[name] = array.copy()
+
+    # Transfer all point data arrays.
+    for name, array in rectl_grid.point_data.items():
+        explicit_grid.point_data[name] = array.copy()
+
+    # (Optional) Transfer field data as well.
+    for name, array in rectl_grid.field_data.items():
+        explicit_grid.field_data[name] = array.copy()
+
+    return explicit_grid

{subsurface_terra-2025.1.0rc8 → subsurface_terra-2025.1.0rc11}/subsurface/modules/reader/wells/read_borehole_interface.py

@@ -100,6 +100,16 @@ def _validate_lith_data(d: pd.DataFrame, reader_helper: GenericReaderFilesHelper
         raise AttributeError('If wells attributes represent lithology, `component lith` column must be present in the file. '
                              'Use columns_map to assign column names to these fields. Maybe you are marking as lithology'
                              'the wrong file?')
+    else:
+        # TODO: Add categories to reader helper
+        categories = sorted(d['component lith'].dropna().unique())
+        d['component lith'] = pd.Categorical(
+            d['component lith'],
+            categories=categories,
+            ordered=True
+        )
+        
+        d['lith_ids'] = d['component lith'].cat.codes + 1
 
     given_top = np.isin(['top', 'base'], d.columns).all()
     given_altitude_and_base = np.isin(['altitude', 'base'], d.columns).all()