refactor: Move workflow plugins

docs/geos_posp_docs/PVplugins.rst

@@ -5,59 +5,9 @@ Paraview plugins were developed using Python 3.9.13 and are compatible with Para
 
 The plugins include:
 
-* A reader that parse GEOS output log file;
-* 3D mesh cleanning plugins;
-* Processing plugins to compute additional geomechanical properties;
 * Visualization plugins to plot Mohr's circles and cross plots using Paraview Python View.
 
 
-PVExtractMergeBlocksVolume plugin
--------------------------------------------
-
-.. automodule:: PVplugins.PVExtractMergeBlocksVolume
-
-
-PVExtractMergeBlocksVolumeSurface plugin
---------------------------------------------------
-
-.. automodule:: PVplugins.PVExtractMergeBlocksVolumeSurface
-
-
-PVExtractMergeBlocksVolumeSurfaceWell plugin
-------------------------------------------------------
-
-.. automodule:: PVplugins.PVExtractMergeBlocksVolumeSurfaceWell
-
-
-PVExtractMergeBlocksVolumeWell plugin
------------------------------------------------
-
-.. automodule:: PVplugins.PVExtractMergeBlocksVolumeWell
-
-PVGeomechanicsWorkflowVolume plugin
----------------------------------------------
-
-.. automodule:: PVplugins.PVGeomechanicsWorkflowVolume
-
-
-PVGeomechanicsWorkflowVolumeSurface plugin
-----------------------------------------------------
-
-.. automodule:: PVplugins.PVGeomechanicsWorkflowVolumeSurface
-
-
-PVGeomechanicsWorkflowVolumeSurfaceWell plugin
---------------------------------------------------------
-
-.. automodule:: PVplugins.PVGeomechanicsWorkflowVolumeSurfaceWell
-
-
-PVGeomechanicsWorkflowVolumeWell plugin
--------------------------------------------------
-
-.. automodule:: PVplugins.PVGeomechanicsWorkflowVolumeWell
-
-
 PVMohrCirclePlot plugin
 ---------------------------------
 

docs/geos_pv_docs/processing.rst

@@ -1,5 +1,12 @@
 Post-/Pre-processing
 =========================
+The plugins include:
+
+* A reader that parse GEOS output log file;
+* 3D mesh cleanning plugins;
+* Processing plugins to compute additional geomechanical properties;
+* Visualization plugins to plot Mohr's circles (currently in `geos_posp`) and cross plots using Paraview Python View.
+
 
 PVAttributeMapping
 --------------------
@@ -19,12 +26,6 @@ PVFillPartialArrays
 .. automodule:: geos.pv.plugins.PVFillPartialArrays
 
 
-PVGeomechanicsCalculator plugin
----------------------------------------
-
-.. automodule:: geos.pv.plugins.PVGeomechanicsCalculator
-
-
 PVSplitMesh
 ----------------------------------
 
@@ -41,3 +42,65 @@ PVClipToMainFrame
 ----------------------------------
 
 .. automodule:: geos.pv.plugins.PVClipToMainFrame
+
+
+Geos output pre-processing
++++++++++++++++++++++++++++++
+
+PVExtractMergeBlocksVolume plugin
+-------------------------------------------
+
+.. automodule:: geos.pv.plugins.PVExtractMergeBlocksVolume
+
+
+PVExtractMergeBlocksVolumeSurface plugin
+--------------------------------------------------
+
+.. automodule:: geos.pv.plugins.PVExtractMergeBlocksVolumeSurface
+
+
+PVExtractMergeBlocksVolumeSurfaceWell plugin
+------------------------------------------------------
+
+.. automodule:: geos.pv.plugins.PVExtractMergeBlocksVolumeSurfaceWell
+
+
+PVExtractMergeBlocksVolumeWell plugin
+-----------------------------------------------
+
+.. automodule:: geos.pv.plugins.PVExtractMergeBlocksVolumeWell
+
+
+
+Geomechanics workflows
+++++++++++++++++++++++++
+
+
+PVGeomechanicsWorkflowVolume plugin
+---------------------------------------------
+
+.. automodule:: geos.pv.plugins.PVGeomechanicsWorkflowVolume
+
+
+PVGeomechanicsWorkflowVolumeSurface plugin
+----------------------------------------------------
+
+.. automodule:: geos.pv.plugins.PVGeomechanicsWorkflowVolumeSurface
+
+
+PVGeomechanicsWorkflowVolumeSurfaceWell plugin
+--------------------------------------------------------
+
+.. automodule:: geos.pv.plugins.PVGeomechanicsWorkflowVolumeSurfaceWell
+
+
+PVGeomechanicsWorkflowVolumeWell plugin
+-------------------------------------------------
+
+.. automodule:: geos.pv.plugins.PVGeomechanicsWorkflowVolumeWell
+
+
+PVGeomechanicsCalculator plugin
+---------------------------------------
+
+.. automodule:: geos.pv.plugins.PVGeomechanicsCalculator

geos-posp/src/PVplugins/PVExtractMergeBlocksVolume.py → geos-pv/src/geos/pv/plugins/PVExtractMergeBlocksVolume.py

@@ -2,20 +2,20 @@
 # SPDX-FileCopyrightText: Copyright 2023-2024 TotalEnergies.
 # SPDX-FileContributor: Martin Lemay
 # ruff: noqa: E402 # disable Module level import not at top of file
-import os
 import sys
+from pathlib import Path
 import numpy as np
 import numpy.typing as npt
 from typing_extensions import Self
 from vtkmodules.vtkCommonCore import vtkInformation, vtkInformationVector
 from vtkmodules.vtkCommonDataModel import vtkMultiBlockDataSet
 
-dir_path = os.path.dirname( os.path.realpath( __file__ ) )
-parent_dir_path = os.path.dirname( dir_path )
-if parent_dir_path not in sys.path:
-    sys.path.append( parent_dir_path )
+# update sys.path to load all GEOS Python Package dependencies
+geos_pv_path: Path = Path( __file__ ).parent.parent.parent.parent.parent
+sys.path.insert( 0, str( geos_pv_path / "src" ) )
+from geos.pv.utils.config import update_paths
 
-import PVplugins  # noqa: F401
+update_paths()
 
 from geos.utils.GeosOutputsConstants import (
     GeosMeshOutputsEnum,
@@ -28,7 +28,7 @@
     copyAttribute,
     createCellCenterAttribute,
 )
-from geos_posp.visu.PVUtils.paraviewTreatments import getTimeStepIndex
+from geos.pv.utils.paraviewTreatments import getTimeStepIndex
 from paraview.util.vtkAlgorithm import (  # type: ignore[import-not-found]
     VTKPythonAlgorithmBase, smdomain, smhint, smproperty, smproxy,
 )

geos-posp/src/PVplugins/PVExtractMergeBlocksVolumeSurface.py → geos-pv/src/geos/pv/plugins/PVExtractMergeBlocksVolumeSurface.py

@@ -2,21 +2,21 @@
 # SPDX-FileCopyrightText: Copyright 2023-2024 TotalEnergies.
 # SPDX-FileContributor: Martin Lemay
 # ruff: noqa: E402 # disable Module level import not at top of file
-import os
 import sys
+from pathlib import Path
 
 import numpy as np
 import numpy.typing as npt
 from typing_extensions import Self
 from vtkmodules.vtkCommonCore import vtkInformation, vtkInformationVector
 from vtkmodules.vtkCommonDataModel import vtkMultiBlockDataSet
 
-dir_path = os.path.dirname( os.path.realpath( __file__ ) )
-parent_dir_path = os.path.dirname( dir_path )
-if parent_dir_path not in sys.path:
-    sys.path.append( parent_dir_path )
+# update sys.path to load all GEOS Python Package dependencies
+geos_pv_path: Path = Path( __file__ ).parent.parent.parent.parent.parent
+sys.path.insert( 0, str( geos_pv_path / "src" ) )
+from geos.pv.utils.config import update_paths
 
-import PVplugins  # noqa: F401
+update_paths()
 
 from geos.utils.GeosOutputsConstants import (
     GeosMeshOutputsEnum,
@@ -29,7 +29,7 @@
     copyAttribute,
     createCellCenterAttribute,
 )
-from geos_posp.visu.PVUtils.paraviewTreatments import getTimeStepIndex
+from geos.pv.utils.paraviewTreatments import getTimeStepIndex
 from paraview.util.vtkAlgorithm import (  # type: ignore[import-not-found]
     VTKPythonAlgorithmBase, smdomain, smhint, smproperty, smproxy,
 )

geos-posp/src/PVplugins/PVExtractMergeBlocksVolumeSurfaceWell.py → geos-pv/src/geos/pv/plugins/PVExtractMergeBlocksVolumeSurfaceWell.py

@@ -2,21 +2,21 @@
 # SPDX-FileCopyrightText: Copyright 2023-2024 TotalEnergies.
 # SPDX-FileContributor: Martin Lemay
 # ruff: noqa: E402 # disable Module level import not at top of file
-import os
 import sys
+from pathlib import Path
 
 import numpy as np
 import numpy.typing as npt
 from typing_extensions import Self
 from vtkmodules.vtkCommonCore import vtkInformation, vtkInformationVector
 from vtkmodules.vtkCommonDataModel import vtkMultiBlockDataSet
 
-dir_path = os.path.dirname( os.path.realpath( __file__ ) )
-parent_dir_path = os.path.dirname( dir_path )
-if parent_dir_path not in sys.path:
-    sys.path.append( parent_dir_path )
+# update sys.path to load all GEOS Python Package dependencies
+geos_pv_path: Path = Path( __file__ ).parent.parent.parent.parent.parent
+sys.path.insert( 0, str( geos_pv_path / "src" ) )
+from geos.pv.utils.config import update_paths
 
-import PVplugins  # noqa: F401
+update_paths()
 
 from geos.utils.GeosOutputsConstants import (
     GeosMeshOutputsEnum,
@@ -29,7 +29,7 @@
     copyAttribute,
     createCellCenterAttribute,
 )
-from geos_posp.visu.PVUtils.paraviewTreatments import getTimeStepIndex
+from geos.pv.utils.paraviewTreatments import getTimeStepIndex
 from paraview.util.vtkAlgorithm import (  # type: ignore[import-not-found]
     VTKPythonAlgorithmBase, smdomain, smhint, smproperty, smproxy,
 )

geos-posp/src/PVplugins/PVExtractMergeBlocksVolumeWell.py → geos-pv/src/geos/pv/plugins/PVExtractMergeBlocksVolumeWell.py

@@ -2,8 +2,8 @@
 # SPDX-FileCopyrightText: Copyright 2023-2024 TotalEnergies.
 # SPDX-FileContributor: Martin Lemay
 # ruff: noqa: E402 # disable Module level import not at top of file
-import os
 import sys
+from pathlib import Path
 
 import numpy as np
 import numpy.typing as npt
@@ -14,12 +14,12 @@
 from vtkmodules.vtkCommonCore import vtkInformation, vtkInformationVector
 from vtkmodules.vtkCommonDataModel import vtkMultiBlockDataSet
 
-dir_path = os.path.dirname( os.path.realpath( __file__ ) )
-parent_dir_path = os.path.dirname( dir_path )
-if parent_dir_path not in sys.path:
-    sys.path.append( parent_dir_path )
+# update sys.path to load all GEOS Python Package dependencies
+geos_pv_path: Path = Path( __file__ ).parent.parent.parent.parent.parent
+sys.path.insert( 0, str( geos_pv_path / "src" ) )
+from geos.pv.utils.config import update_paths
 
-import PVplugins  # noqa: F401
+update_paths()
 
 from geos.utils.GeosOutputsConstants import (
     GeosMeshOutputsEnum,
@@ -32,7 +32,7 @@
     copyAttribute,
     createCellCenterAttribute,
 )
-from geos_posp.visu.PVUtils.paraviewTreatments import getTimeStepIndex
+from geos.pv.utils.paraviewTreatments import getTimeStepIndex
 
 __doc__ = """
 PVExtractMergeBlocksVolumeWell is a Paraview plugin that allows to merge

geos-posp/src/PVplugins/PVGeomechanicsWorkflowVolume.py → geos-pv/src/geos/pv/plugins/PVGeomechanicsWorkflowVolume.py

@@ -2,21 +2,21 @@
 # SPDX-FileCopyrightText: Copyright 2023-2024 TotalEnergies.
 # SPDX-FileContributor: Martin Lemay
 # ruff: noqa: E402 # disable Module level import not at top of file
-import os
 import sys
+from pathlib import Path
 
 import numpy as np
 from typing_extensions import Self
 from vtkmodules.vtkCommonCore import vtkInformation, vtkInformationVector
 from vtkmodules.vtkCommonDataModel import (
     vtkMultiBlockDataSet, )
 
-dir_path = os.path.dirname( os.path.realpath( __file__ ) )
-parent_dir_path = os.path.dirname( dir_path )
-if parent_dir_path not in sys.path:
-    sys.path.append( parent_dir_path )
+# update sys.path to load all GEOS Python Package dependencies
+geos_pv_path: Path = Path( __file__ ).parent.parent.parent.parent.parent
+sys.path.insert( 0, str( geos_pv_path / "src" ) )
+from geos.pv.utils.config import update_paths
 
-import PVplugins  # noqa: F401
+update_paths()
 
 from geos.utils.Logger import Logger, getLogger
 from geos.utils.PhysicalConstants import (
@@ -29,12 +29,9 @@
 from paraview.util.vtkAlgorithm import (  # type: ignore[import-not-found]
     VTKPythonAlgorithmBase, smdomain, smhint, smproperty, smproxy,
 )
-from paraview.detail.loghandler import (  # type: ignore[import-not-found]
-    VTKHandler,
-)  # source: https://github.com/Kitware/ParaView/blob/master/Wrapping/Python/paraview/detail/loghandler.py
 
-from PVplugins.PVExtractMergeBlocksVolume import PVExtractMergeBlocksVolume
-from geos.processing.post_processing.GeomechanicsCalculator import GeomechanicsCalculator
+from geos.pv.plugins.PVExtractMergeBlocksVolume import PVExtractMergeBlocksVolume
+from geos.pv.plugins.PVGeomechanicsCalculator import PVGeomechanicsCalculator
 
 __doc__ = """
 PVGeomechanicsWorkflowVolume is a Paraview plugin that execute multiple filters
@@ -372,16 +369,14 @@ def computeAdditionalOutputsVolume( self: Self ) -> bool:
         Returns:
             bool: True if calculation successfully eneded, False otherwise.
         """
-        filter = GeomechanicsCalculator( self.m_volumeMesh,
-                                         computeAdvancedOutputs=self.getComputeAdvancedOutputs(),
-                                         speHandler=True )
-        if not filter.logger.hasHandlers():
-            filter.setLoggerHandler( VTKHandler() )
-        filter.physicalConstants.grainBulkModulus = self.grainBulkModulus
-        filter.physicalConstants.specificDensity = self.specificDensity
-        filter.physicalConstants.rockCohesion = self.rockCohesion
-        filter.physicalConstants.frictionAngle = self.frictionAngle
-        filter.applyFilter()
-        self.m_volumeMesh.ShallowCopy( filter.getOutput() )
+        filter = PVGeomechanicsCalculator()
+        filter.SetInputDataObject( self.m_volumeMesh ),
+        filter.setComputeAdvancedProperties( self.getComputeAdvancedOutputs() )
+        filter.setGrainBulkModulus( self.m_grainBulkModulus )
+        filter.setSpecificDensity = ( self.m_specificDensity )
+        filter.setRockCohesion = ( self.m_rockCohesion )
+        filter.setFrictionAngle = ( self.m_frictionAngle )
+        filter.Update()
+        self.m_volumeMesh.ShallowCopy( filter.GetOutputDataObject( 0 ) )
         self.m_volumeMesh.Modified()
         return True