refactor: Move GeosBlockExtractor from geos-posp to geos-proccessing

docs/geos_mesh_docs/processing.rst

@@ -27,6 +27,7 @@ geos.mesh.processing.FillPartialArrays filter
     :undoc-members:
     :show-inheritance:
 
+
 geos.mesh.processing.meshQualityMetricHelpers module
 -----------------------------------------------------
 

docs/geos_posp_docs/filters.rst

@@ -3,14 +3,6 @@ vtk Filters
 
 This package defines vtk filters that allows to process Geos outputs.
 
-geos_posp.filters.GeosBlockExtractor module
------------------------------------------------
-
-.. automodule:: geos_posp.filters.GeosBlockExtractor
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
 geos_posp.filters.GeosBlockMerge module
 -------------------------------------------
 

docs/geos_processing_docs/post_processing.rst

@@ -12,4 +12,12 @@ geos.processing.post_processing.GeomechanicsCalculator module
 .. automodule:: geos.processing.post_processing.GeomechanicsCalculator
    :members:
    :undoc-members:
-   :show-inheritance:
+   :show-inheritance:
+
+geos.processing.post_processing.GeosBlockExtractor module
+----------------------------------------------------------
+
+.. automodule:: geos.processing.post_processing.GeosBlockExtractor
+   :members:
+   :undoc-members:
+   :show-inheritance:

geos-mesh/src/geos/mesh/utils/arrayHelpers.py

@@ -26,6 +26,58 @@
 """
 
 
+def getCellDimension( mesh: Union[ vtkMultiBlockDataSet, vtkDataSet ] ) -> set[ int ]:
+    """Get the set of the different cells dimension of a mesh.
+
+    Args:
+        mesh (Union[vtkMultiBlockDataSet, vtkDataSet]): The input mesh with the cells dimension to get.
+
+    Returns:
+        set[int]: The set of the different cells dimension in the input mesh.
+    """
+    if isinstance( mesh, vtkDataSet ):
+        return getCellDimensionDataSet( mesh )
+    elif isinstance( mesh, vtkMultiBlockDataSet ):
+        return getCellDimensionMultiBlockDataSet( mesh )
+    else:
+        raise TypeError( "The input mesh must be a vtkMultiBlockDataSet or a vtkDataSet." )
+
+
+def getCellDimensionMultiBlockDataSet( multiBlockDataSet: vtkMultiBlockDataSet ) -> set[ int ]:
+    """Get the set of the different cells dimension of a multiBlockDataSet.
+
+    Args:
+        multiBlockDataSet (vtkMultiBlockDataSet): The input mesh with the cells dimension to get.
+
+    Returns:
+        set[int]: The set of the different cells dimension in the input multiBlockDataSet.
+    """
+    cellDim: set[ int ] = set()
+    listFlatIdDataSet: list[ int ] = getBlockElementIndexesFlatten( multiBlockDataSet )
+    for flatIdDataSet in listFlatIdDataSet:
+        dataSet: vtkDataSet = vtkDataSet.SafeDownCast( multiBlockDataSet.GetDataSet( flatIdDataSet ) )
+        cellDim = cellDim.union( getCellDimensionDataSet( dataSet ) )
+    return cellDim
+
+
+def getCellDimensionDataSet( dataSet: vtkDataSet ) -> set[ int ]:
+    """Get the set of the different cells dimension of a dataSet.
+
+    Args:
+        dataSet (vtkDataSet): The input mesh with the cells dimension to get.
+
+    Returns:
+        set[int]: The set of the different cells dimension in the input dataSet.
+    """
+    cellDim: set[ int ] = set()
+    cellIter = dataSet.NewCellIterator()
+    cellIter.InitTraversal()
+    while not cellIter.IsDoneWithTraversal():
+        cellDim.add( cellIter.GetCellDimension() )
+        cellIter.GoToNextCell()
+    return cellDim
+
+
 def computeElementMapping(
     meshFrom: Union[ vtkDataSet, vtkMultiBlockDataSet ],
     meshTo: Union[ vtkDataSet, vtkMultiBlockDataSet ],

geos-mesh/src/geos/mesh/utils/multiblockHelpers.py

@@ -190,29 +190,6 @@ def getBlockFromFlatIndex( multiBlockDataSet: Union[ vtkMultiBlockDataSet, vtkCo
     return None
 
 
-def getBlockFromName( multiBlockDataSet: Union[ vtkMultiBlockDataSet, vtkCompositeDataSet ],
-                      blockName: str ) -> Union[ None, vtkDataObject ]:
-    """Get the block named blockName from the vtkMultiBlockDataSet.
-
-    Args:
-        multiBlockDataSet (vtkMultiBlockDataSet | vtkCompositeDataSet): MultiBlockDataSet with the block to get.
-        blockName (str): The name of the block to get.
-
-    Returns:
-        Union[None, vtkDataObject]: The block name blockName if it exists, None otherwise
-    """
-    # initialize data object tree iterator
-    iterator: vtkDataObjectTreeIterator = vtkDataObjectTreeIterator()
-    iterator.SetDataSet( multiBlockDataSet )
-    iterator.VisitOnlyLeavesOff()
-    iterator.GoToFirstItem()
-    while iterator.GetCurrentDataObject() is not None:
-        if iterator.GetCurrentMetaData().Get( vtkMultiBlockDataSet.NAME() ) == blockName:
-            return iterator.GetCurrentDataObject()
-        iterator.GoToNextItem()
-    return None
-
-
 def extractBlock( multiBlockDataSet: vtkMultiBlockDataSet, blockIndex: int ) -> vtkMultiBlockDataSet:
     """Extract the block with index blockIndex from multiBlockDataSet.
 

geos-mesh/tests/conftest.py

@@ -10,7 +10,7 @@
 import numpy.typing as npt
 
 from vtkmodules.vtkCommonDataModel import vtkDataSet, vtkMultiBlockDataSet, vtkPolyData
-from vtkmodules.vtkIOXML import vtkXMLGenericDataObjectReader, vtkXMLMultiBlockDataReader
+from vtkmodules.vtkIOXML import vtkXMLGenericDataObjectReader
 
 
 @pytest.fixture
@@ -178,6 +178,10 @@ def _get_dataset( datasetType: str ) -> Union[ vtkMultiBlockDataSet, vtkPolyData
             vtkFilename = "data/fracture_res5_id.vtp"
         elif datasetType == "emptypolydata":
             vtkFilename = "data/fracture_res5_id_empty.vtp"
+        elif datasetType == "meshGeosExtractBlockTmp":
+            vtkFilename = "data/meshGeosExtractBlockTmp.vtm"
+        elif datasetType == "well":
+            vtkFilename = "data/well.vtu"
         datapath: str = os.path.join( os.path.dirname( os.path.realpath( __file__ ) ), vtkFilename )
         reader.SetFileName( datapath )
         reader.Update()

geos-mesh/tests/data/meshGeosExtractBlockTmp.vtm

@@ -0,0 +1,16 @@
+<?xml version="1.0"?>
+<VTKFile type="vtkMultiBlockDataSet" version="1.0">
+    <vtkMultiBlockDataSet>
+        <Block name="CellElementRegion">
+            <DataSet name="domain" file="domain_res5_id.vtu"/>
+            <DataSet name="emptyDomain" file="domain_res5_id_empty.vtu"/>
+        </Block>
+        <Block name="SurfaceElementRegion">
+            <DataSet name="fracture" file="fracture_res5_id.vtu"/>
+            <DataSet name="emptyFracture" file="fracture_res5_id_empty.vtu"/>
+        </Block>
+        <Block name="WellElementRegion">
+            <DataSet name="well" file="well.vtu"/>
+        </Block>
+    </vtkMultiBlockDataSet>
+</VTKFile>

geos-mesh/tests/data/well.vtu

@@ -0,0 +1,48 @@
+<VTKFile type="UnstructuredGrid" version="1.0" byte_order="LittleEndian" header_type="UInt64" compressor="vtkZLibDataCompressor">
+  <UnstructuredGrid>
+    <Piece NumberOfPoints="11" NumberOfCells="10">
+      <PointData>
+        <DataArray type="Float32" Name="DistanceToCenter" format="binary" RangeMin="0" RangeMax="5">
+          AQAAAAAAAAAAgAAAAAAAACwAAAAAAAAAIQAAAAAAAAA=eF5jYFjgwMDQAMQOQMwAYtszgAGYhoqD5Bc4AACHAgY/
+        </DataArray>
+        <DataArray type="Float32" Name="Polynomial" format="binary" RangeMin="1" RangeMax="11">
+          AQAAAAAAAAAAgAAAAAAAACwAAAAAAAAAKAAAAAAAAAA=eF5jYGiwZ2BgcAAiIG4A4gVAfACIHwAxgyMDgwAQKwCxgSMAmJ8GpA==
+        </DataArray>
+      </PointData>
+      <CellData>
+      </CellData>
+      <Points>
+        <DataArray type="Float32" Name="Points" NumberOfComponents="3" format="binary" RangeMin="0" RangeMax="10">
+          AQAAAAAAAAAAgAAAAAAAAIQAAAAAAAAAKQAAAAAAAAA=eF5jYEAGDfZIHAckJhK7AYm9AIl9AIn9AInN4IhgCiCxFeBsAJt9BjM=
+          <InformationKey name="L2_NORM_FINITE_RANGE" location="vtkDataArray" length="2">
+            <Value index="0">
+              0
+            </Value>
+            <Value index="1">
+              10
+            </Value>
+          </InformationKey>
+          <InformationKey name="L2_NORM_RANGE" location="vtkDataArray" length="2">
+            <Value index="0">
+              0
+            </Value>
+            <Value index="1">
+              10
+            </Value>
+          </InformationKey>
+        </DataArray>
+      </Points>
+      <Cells>
+        <DataArray type="Int64" Name="connectivity" format="binary" RangeMin="0" RangeMax="10">
+          AQAAAAAAAAAAgAAAAAAAAKAAAAAAAAAAJgAAAAAAAAA=eF5dxTkCABAMALA6i/8/2MCULIl4Cldu3Hnw5OTFm8//Ahb4AGU=
+        </DataArray>
+        <DataArray type="Int64" Name="offsets" format="binary" RangeMin="2" RangeMax="20">
+          AQAAAAAAAAAAgAAAAAAAAFAAAAAAAAAAIwAAAAAAAAA=eF5jYoAAFijNBqU5oDQXlOaB0nxQWgBKC0FpESgNAA4QAG8=
+        </DataArray>
+        <DataArray type="UInt8" Name="types" format="binary" RangeMin="3" RangeMax="3">
+          AQAAAAAAAAAAgAAAAAAAAAoAAAAAAAAACwAAAAAAAAA=eF5jZoYBAACvAB8=
+        </DataArray>
+      </Cells>
+    </Piece>
+  </UnstructuredGrid>
+</VTKFile>

geos-mesh/tests/test_arrayHelpers.py

@@ -19,6 +19,23 @@
 from geos.mesh.utils.arrayModifiers import createConstantAttribute
 
 
+@pytest.mark.parametrize( "meshName, cellDimExpected", [
+    ( "dataset", { 3 } ),
+    ( "fracture", { 2 } ),
+    ( "well", { 1 } ),
+    ( "meshGeosExtractBlockTmp", { 3, 2, 1 } ),
+] )
+def test_getCellDimension(
+    dataSetTest: vtkDataSet,
+    meshName: str,
+    cellDimExpected: set[ int ],
+) -> None:
+    """Test getting the different cells dimension in a mesh."""
+    mesh: Union[ vtkDataSet, vtkMultiBlockDataSet ] = dataSetTest( meshName )
+    cellDimObtained: set[ int ] = arrayHelpers.getCellDimension( mesh )
+    assert cellDimObtained == cellDimExpected
+
+
 @pytest.mark.parametrize( "meshFromName, meshToName, points", [
     ( "multiblock", "emptymultiblock", False ),
     ( "multiblock", "emptyFracture", False ),

geos-posp/src/PVplugins/PVExtractMergeBlocksVolume.py

@@ -22,7 +22,7 @@
     getAttributeToTransferFromInitialTime,
 )
 from geos.utils.Logger import ERROR, INFO, Logger, getLogger
-from geos_posp.filters.GeosBlockExtractor import GeosBlockExtractor
+from geos.processing.post_processing.GeosBlockExtractor import GeosBlockExtractor
 from geos_posp.filters.GeosBlockMerge import GeosBlockMerge
 from geos.mesh.utils.arrayModifiers import (
     copyAttribute,
@@ -277,13 +277,11 @@ def doExtractAndMerge( self: Self, input: vtkMultiBlockDataSet, output: vtkMulti
             bool: True if extraction and merge successfully eneded, False otherwise
         """
         # extract blocks
-        blockExtractor: GeosBlockExtractor = GeosBlockExtractor()
-        blockExtractor.SetLogger( self.m_logger )
-        blockExtractor.SetInputDataObject( input )
-        blockExtractor.Update()
+        blockExtractor: GeosBlockExtractor = GeosBlockExtractor( input )
+        blockExtractor.applyFilter()
 
         # recover output objects from GeosBlockExtractor filter
-        volumeBlockExtracted: vtkMultiBlockDataSet = blockExtractor.getOutputVolume()
+        volumeBlockExtracted: vtkMultiBlockDataSet = blockExtractor.extractedGeosDomain.volume
         assert volumeBlockExtracted is not None, "Extracted Volume mesh is null."
 
         # merge internal blocks

geos-posp/src/PVplugins/PVExtractMergeBlocksVolumeSurface.py

@@ -23,7 +23,7 @@
     getAttributeToTransferFromInitialTime,
 )
 from geos.utils.Logger import ERROR, INFO, Logger, getLogger
-from geos_posp.filters.GeosBlockExtractor import GeosBlockExtractor
+from geos.processing.post_processing.GeosBlockExtractor import GeosBlockExtractor
 from geos_posp.filters.GeosBlockMerge import GeosBlockMerge
 from geos.mesh.utils.arrayModifiers import (
     copyAttribute,
@@ -292,15 +292,12 @@ def doExtractAndMerge(
             bool: True if extraction and merge successfully eneded, False otherwise
         """
         # extract blocks
-        blockExtractor: GeosBlockExtractor = GeosBlockExtractor()
-        blockExtractor.SetLogger( self.m_logger )
-        blockExtractor.SetInputDataObject( input )
-        blockExtractor.ExtractFaultsOn()
-        blockExtractor.Update()
+        blockExtractor: GeosBlockExtractor = GeosBlockExtractor( input, extractFault=True )
+        blockExtractor.applyFilter()
 
         # recover output objects from GeosBlockExtractor filter
-        volumeBlockExtracted: vtkMultiBlockDataSet = blockExtractor.getOutputVolume()
-        faultBlockExtracted: vtkMultiBlockDataSet = blockExtractor.getOutputFaults()
+        volumeBlockExtracted: vtkMultiBlockDataSet = blockExtractor.extractedGeosDomain.volume
+        faultBlockExtracted: vtkMultiBlockDataSet = blockExtractor.extractedGeosDomain.fault
 
         # rename attributes and merge blocks
         assert volumeBlockExtracted is not None, "Extracted Volume mesh is null."

geos-posp/src/PVplugins/PVExtractMergeBlocksVolumeSurfaceWell.py

@@ -23,7 +23,7 @@
     getAttributeToTransferFromInitialTime,
 )
 from geos.utils.Logger import ERROR, INFO, Logger, getLogger
-from geos_posp.filters.GeosBlockExtractor import GeosBlockExtractor
+from geos.processing.post_processing.GeosBlockExtractor import GeosBlockExtractor
 from geos_posp.filters.GeosBlockMerge import GeosBlockMerge
 from geos.mesh.utils.arrayModifiers import (
     copyAttribute,
@@ -316,23 +316,19 @@ def doExtractAndMerge(
             bool: True if extraction and merge successfully eneded, False otherwise
         """
         # extract blocks
-        blockExtractor: GeosBlockExtractor = GeosBlockExtractor()
-        blockExtractor.SetLogger( self.m_logger )
-        blockExtractor.SetInputDataObject( input )
-        blockExtractor.ExtractFaultsOn()
-        blockExtractor.ExtractWellsOn()
-        blockExtractor.Update()
+        blockExtractor: GeosBlockExtractor = GeosBlockExtractor( input, extractFaults=True, extractWells=True )
+        blockExtractor.applyFilter()
 
         # recover output objects from GeosBlockExtractor filter and merge internal blocks
-        volumeBlockExtracted: vtkMultiBlockDataSet = blockExtractor.getOutputVolume()
+        volumeBlockExtracted: vtkMultiBlockDataSet = blockExtractor.extractedGeosDomain.volume
         assert volumeBlockExtracted is not None, "Extracted Volume mesh is null."
         outputCells.ShallowCopy( self.mergeBlocksFilter( volumeBlockExtracted, False ) )
 
-        faultBlockExtracted: vtkMultiBlockDataSet = blockExtractor.getOutputFaults()
+        faultBlockExtracted: vtkMultiBlockDataSet = blockExtractor.extractedGeosDomain.fault
         assert faultBlockExtracted is not None, "Extracted Fault mesh is null."
         outputFaults.ShallowCopy( self.mergeBlocksFilter( faultBlockExtracted, True ) )
 
-        wellBlockExtracted: vtkMultiBlockDataSet = blockExtractor.getOutputWells()
+        wellBlockExtracted: vtkMultiBlockDataSet = blockExtractor.extractedGeosDomain.well
         assert wellBlockExtracted is not None, "Extracted Well mesh is null."
         outputWells.ShallowCopy( self.mergeBlocksFilter( wellBlockExtracted, False ) )
 

geos-posp/src/PVplugins/PVExtractMergeBlocksVolumeWell.py

@@ -26,7 +26,7 @@
     getAttributeToTransferFromInitialTime,
 )
 from geos.utils.Logger import ERROR, INFO, Logger, getLogger
-from geos_posp.filters.GeosBlockExtractor import GeosBlockExtractor
+from geos.processing.post_processing.GeosBlockExtractor import GeosBlockExtractor
 from geos_posp.filters.GeosBlockMerge import GeosBlockMerge
 from geos.mesh.utils.arrayModifiers import (
     copyAttribute,
@@ -302,19 +302,15 @@ def doExtractAndMerge(
             bool: True if extraction and merge successfully eneded, False otherwise
         """
         # extract blocks
-        blockExtractor: GeosBlockExtractor = GeosBlockExtractor()
-        blockExtractor.SetLogger( self.m_logger )
-        blockExtractor.SetInputDataObject( input )
-        blockExtractor.ExtractFaultsOff()
-        blockExtractor.ExtractWellsOn()
-        blockExtractor.Update()
+        blockExtractor: GeosBlockExtractor = GeosBlockExtractor( input, extractWells=True )
+        blockExtractor.applyFilter()
 
         # recover output objects from GeosBlockExtractor filter and merge internal blocks
-        volumeBlockExtracted: vtkMultiBlockDataSet = blockExtractor.getOutputVolume()
+        volumeBlockExtracted: vtkMultiBlockDataSet = blockExtractor.extractedGeosDomain.volume
         assert volumeBlockExtracted is not None, "Extracted Volume mesh is null."
         outputCells.ShallowCopy( self.mergeBlocksFilter( volumeBlockExtracted, False ) )
 
-        wellBlockExtracted: vtkMultiBlockDataSet = blockExtractor.getOutputWells()
+        wellBlockExtracted: vtkMultiBlockDataSet = blockExtractor.extractedGeosDomain.well
         assert wellBlockExtracted is not None, "Extracted Well mesh is null."
         outputWells.ShallowCopy( self.mergeBlocksFilter( wellBlockExtracted, False ) )