subsurface-terra 2025.1.0rc10__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-2025.1.0rc10/subsurface_terra.egg-info → subsurface_terra-2025.1.0rc11}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: subsurface_terra
-Version: 2025.1.0rc10
+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-2025.1.0rc10 → subsurface_terra-2025.1.0rc11}/requirements/requirements_wells.txt

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

{subsurface_terra-2025.1.0rc10 → subsurface_terra-2025.1.0rc11}/subsurface/_version.py

@@ -17,5 +17,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '2025.1.0rc10'
+__version__ = version = '2025.1.0rc11'
 __version_tuple__ = version_tuple = (2025, 1, 0)

{subsurface_terra-2025.1.0rc10 → 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-2025.1.0rc10 → 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-2025.1.0rc10 → subsurface_terra-2025.1.0rc11}/subsurface/modules/reader/volume/read_volume.py

@@ -102,21 +102,81 @@ def read_volumetric_mesh_attr_file(reader_helper: GenericReaderFilesHelper) -> p
     return df
 
 
-def pv_cast_to_explicit_structured_grid(pyvista_object):
-
+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()

{subsurface_terra-2025.1.0rc10 → 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()

subsurface_terra-2025.1.0rc11/subsurface/modules/tools/mocking_aux.py

@@ -0,0 +1,104 @@
+import numpy as np
+import pyvista as pv
+
+
+def transform_gaussian_blur(grid, sigma=20.0):
+    """
+    Applies a Gaussian blur to the 'model_name' field of the structured grid.
+
+    Parameters:
+        grid - PyVista grid with 'model_name' field
+        sigma - Standard deviation for the Gaussian kernel
+    """
+    from scipy.ndimage import gaussian_filter
+
+    # Get the original dimensions of the grid
+    dims = grid.dimensions
+
+    # Reshape the data to 3D array matching grid dimensions
+    values = np.array(grid['model_name'])
+    values_3d = values.reshape(dims[2] - 1, dims[1] - 1, dims[0] - 1).transpose(2, 1, 0)
+
+    # Apply Gaussian filter
+    blurred_values = gaussian_filter(values_3d, sigma=sigma, axes=(2,))
+
+    # Reshape back to 1D array
+    grid['model_name'] = blurred_values.transpose(2, 1, 0).flatten()
+    return grid
+
+
+def transform_sinusoidal(values, amplitude=1.0, frequency=0.01, phase=0):
+    """
+    Apply a sinusoidal transformation to the values.
+    """
+    return values + amplitude * np.sin(frequency * values + phase)
+
+
+def obfuscate_model_name(grid, transform_functions, attr):
+    """
+    Applies transformation functions to the 'model_name' field.
+    Functions can operate on either the grid or the values array.
+    """
+    for func in transform_functions:
+        if 'grid' in func.__code__.co_varnames:
+            # Function expects the full grid
+            grid = func(grid)
+        else:
+            # Function expects just the values array
+            values = np.array(grid[attr])
+            grid[attr] = func(values)
+
+    return grid
+
+
+# pyvista_struct = transform_xy_to_z_propagation(pyvista_struct, z_factor=0.3, noise_level=0.1)
+def transform_subtract_mean(values):
+    """
+    Subtract the mean of the array from each element.
+    """
+    return values - np.mean(values)
+
+
+def transform_scale(values, scale_factor=0.003):
+    """
+    Multiply each value by scale_factor.
+    """
+    return values * scale_factor
+
+
+
+
+def update_extent(pyvista_grid, new_extent):
+    # new_extent: array-like with 6 elements [xmin, xmax, ymin, ymax, zmin, zmax]
+    old_bounds = np.array(pyvista_grid.bounds)  # [xmin, xmax, ymin, ymax, zmin, zmax]
+
+    # Check for valid extents
+    if any(new_extent[i] >= new_extent[i + 1] for i in range(0, 6, 2)):
+        raise ValueError("Each min value must be less than the corresponding max value in the new extent.")
+
+    # Compute old ranges and new ranges for each axis
+    old_ranges = old_bounds[1::2] - old_bounds[0::2]  # [x_range, y_range, z_range]
+    new_ranges = np.array([new_extent[1] - new_extent[0],
+                           new_extent[3] - new_extent[2],
+                           new_extent[5] - new_extent[4]])
+
+    # Avoid division by zero if any old range is zero
+    if np.any(old_ranges == 0):
+        raise ValueError("One of the dimensions in the current grid has zero length.")
+
+    # Get the old points and reshape for easier manipulation
+    old_points = pyvista_grid.points  # shape (N, 3)
+
+    # Compute normalized coordinates within the old extent
+    norm_points = (old_points - old_bounds[0::2]) / old_ranges
+
+    # Compute new points based on new extent
+    new_mins = np.array([new_extent[0], new_extent[2], new_extent[4]])
+    new_points = new_mins + norm_points * new_ranges
+
+    # Update the grid's points
+    pyvista_grid.points = new_points
+
+    # Updating bounds is implicit once the points are modified.
+    pyvista_grid.Modified()
+    return pyvista_grid

{subsurface_terra-2025.1.0rc10 → subsurface_terra-2025.1.0rc11/subsurface_terra.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: subsurface_terra
-Version: 2025.1.0rc10
+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-2025.1.0rc10 → subsurface_terra-2025.1.0rc11}/subsurface_terra.egg-info/SOURCES.txt

@@ -2,6 +2,13 @@
 LICENSE
 README.rst
 setup.py
+.teamcity/Subsurface/project-config.xml
+.teamcity/Subsurface/buildTypes/Subsurface_ReleaseSubsurface.xml
+.teamcity/Subsurface/buildTypes/Subsurface_ReleaseSubsurface_2.xml
+.teamcity/Subsurface/buildTypes/Subsurface_Testing.xml
+.teamcity/Subsurface/vcsRoots/Subsurface_HttpsGithubComTerranigmaSolutionsSubsurfaceRefsHeadsMain.xml
+.teamcity/Subsurface/vcsRoots/Subsurface_HttpsGithubComTerranigmaSolutionsSubsurfaceRefsHeadsMain1.xml
+.teamcity/Subsurface/vcsRoots/Subsurface_HttpsGithubComTerranigmaSolutionsSubsurfaceRefsHeadsMain2.xml
 requirements/requirements.txt
 requirements/requirements_all.txt
 requirements/requirements_dev.txt
@@ -92,6 +99,8 @@ subsurface/modules/reader/wells/DEP/_well_files_reader.py
 subsurface/modules/reader/wells/DEP/_wells_api.py
 subsurface/modules/reader/wells/DEP/_welly_reader.py
 subsurface/modules/reader/wells/DEP/pandas_to_welly.py
+subsurface/modules/tools/__init__.py
+subsurface/modules/tools/mocking_aux.py
 subsurface/modules/visualization/__init__.py
 subsurface/modules/visualization/to_pyvista.py
 subsurface/modules/writer/__init__.py