feat: improve and update of geos-mesh utils functions

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

@@ -29,8 +29,7 @@ def mergeBlocks(
 
     """
     if keepPartialAttributes:
-        fillAllPartialAttributes( input, False )
-        fillAllPartialAttributes( input, True )
+        fillAllPartialAttributes( input )
 
     af = vtkAppendDataSets()
     af.MergePointsOn()

geos-mesh/tests/conftest.py

@@ -5,7 +5,7 @@
 # ruff: noqa: E402 # disable Module level import not at top of file
 import os
 import pytest
-from typing import Union
+from typing import Union, Any
 import numpy as np
 import numpy.typing as npt
 
@@ -15,6 +15,7 @@
 
 @pytest.fixture
 def arrayExpected( request: pytest.FixtureRequest ) -> npt.NDArray[ np.float64 ]:
+    """Get an array from a file."""
     reference_data = "data/data.npz"
     reference_data_path = os.path.join( os.path.dirname( os.path.realpath( __file__ ) ), reference_data )
     data = np.load( reference_data_path )
@@ -24,6 +25,7 @@ def arrayExpected( request: pytest.FixtureRequest ) -> npt.NDArray[ np.float64 ]
 
 @pytest.fixture
 def arrayTest( request: pytest.FixtureRequest ) -> npt.NDArray[ np.float64 ]:
+    """Get a random array of float64."""
     np.random.seed( 42 )
     array: npt.NDArray[ np.float64 ] = np.random.rand(
         request.param,
@@ -33,22 +35,150 @@ def arrayTest( request: pytest.FixtureRequest ) -> npt.NDArray[ np.float64 ]:
 
 
 @pytest.fixture
-def dataSetTest() -> Union[ vtkMultiBlockDataSet, vtkPolyData, vtkDataSet ]:
+def getArrayWithSpeTypeValue() -> Any:
+    """Get a random array of input type with the function _getarray().
 
-    def _get_dataset( datasetType: str ):
+    Returns:
+        npt.NDArray[Any]: Random array of input type.
+    """
+
+    def _getarray( nb_component: int, nb_elements: int, valueType: str ) -> Any:
+        """Get a random array of input type.
+
+        Args:
+            nb_component (int): Number of components.
+            nb_elements (int): Number of elements.
+            valueType (str): The type of the value.
+
+        Returns:
+            npt.NDArray[Any]: Random array of input type.
+        """
+        np.random.seed( 28 )
+        if valueType == "int8":
+            if nb_component == 1:
+                return np.array( [ np.int8( 10 * np.random.random() ) for _ in range( nb_elements ) ] )
+            else:
+                return np.array( [ [ np.int8( 10 * np.random.random() ) for _ in range( nb_component ) ]
+                                   for _ in range( nb_elements ) ] )
+
+        elif valueType == "int16":
+            if nb_component == 1:
+                return np.array( [ np.int16( 1000 * np.random.random() ) for _ in range( nb_elements ) ] )
+            else:
+                return np.array( [ [ np.int16( 1000 * np.random.random() ) for _ in range( nb_component ) ]
+                                   for _ in range( nb_elements ) ] )
+
+        elif valueType == "int32":
+            if nb_component == 1:
+                return np.array( [ np.int32( 1000 * np.random.random() ) for _ in range( nb_elements ) ] )
+            else:
+                return np.array( [ [ np.int32( 1000 * np.random.random() ) for _ in range( nb_component ) ]
+                                   for _ in range( nb_elements ) ] )
+
+        elif valueType == "int64":
+            if nb_component == 1:
+                return np.array( [ np.int64( 1000 * np.random.random() ) for _ in range( nb_elements ) ] )
+            else:
+                return np.array( [ [ np.int64( 1000 * np.random.random() ) for _ in range( nb_component ) ]
+                                   for _ in range( nb_elements ) ] )
+
+        if valueType == "uint8":
+            if nb_component == 1:
+                return np.array( [ np.uint8( 10 * np.random.random() ) for _ in range( nb_elements ) ] )
+            else:
+                return np.array( [ [ np.uint8( 10 * np.random.random() ) for _ in range( nb_component ) ]
+                                   for _ in range( nb_elements ) ] )
+
+        elif valueType == "uint16":
+            if nb_component == 1:
+                return np.array( [ np.uint16( 1000 * np.random.random() ) for _ in range( nb_elements ) ] )
+            else:
+                return np.array( [ [ np.uint16( 1000 * np.random.random() ) for _ in range( nb_component ) ]
+                                   for _ in range( nb_elements ) ] )
+
+        elif valueType == "uint32":
+            if nb_component == 1:
+                return np.array( [ np.uint32( 1000 * np.random.random() ) for _ in range( nb_elements ) ] )
+            else:
+                return np.array( [ [ np.uint32( 1000 * np.random.random() ) for _ in range( nb_component ) ]
+                                   for _ in range( nb_elements ) ] )
+
+        elif valueType == "uint64":
+            if nb_component == 1:
+                return np.array( [ np.uint64( 1000 * np.random.random() ) for _ in range( nb_elements ) ] )
+            else:
+                return np.array( [ [ np.uint64( 1000 * np.random.random() ) for _ in range( nb_component ) ]
+                                   for _ in range( nb_elements ) ] )
+
+        elif valueType == "int":
+            if nb_component == 1:
+                return np.array( [ int( 1000 * np.random.random() ) for _ in range( nb_elements ) ] )
+            else:
+                return np.array( [ [ int( 1000 * np.random.random() ) for _ in range( nb_component ) ]
+                                   for _ in range( nb_elements ) ] )
+
+        elif valueType == "float":
+            if nb_component == 1:
+                return np.array( [ float( 1000 * np.random.random() ) for _ in range( nb_elements ) ] )
+            else:
+                return np.array( [ [ float( 1000 * np.random.random() ) for _ in range( nb_component ) ]
+                                   for _ in range( nb_elements ) ] )
+
+        elif valueType == "float32":
+            if nb_component == 1:
+                return np.array( [ np.float32( 1000 * np.random.random() ) for _ in range( nb_elements ) ] )
+            else:
+                return np.array( [ [ np.float32( 1000 * np.random.random() ) for _ in range( nb_component ) ]
+                                   for _ in range( nb_elements ) ] )
+
+        elif valueType == "float64":
+            if nb_component == 1:
+                return np.array( [ np.float64( 1000 * np.random.random() ) for _ in range( nb_elements ) ] )
+            else:
+                return np.array( [ [ np.float64( 1000 * np.random.random() ) for _ in range( nb_component ) ]
+                                   for _ in range( nb_elements ) ] )
+
+    return _getarray
+
+
+@pytest.fixture
+def dataSetTest() -> Any:
+    """Get a vtkObject from a file with the function _get_dataset().
+
+    Returns:
+        (vtkMultiBlockDataSet, vtkPolyData, vtkDataSet): The vtk object.
+    """
+
+    def _get_dataset( datasetType: str ) -> Union[ vtkMultiBlockDataSet, vtkPolyData, vtkDataSet ]:
+        """Get a vtkObject from a file.
+
+        Args:
+            datasetType (str): The type of vtk object wanted.
+
+        Returns:
+            (vtkMultiBlockDataSet, vtkPolyData, vtkDataSet): The vtk object.
+        """
+        reader: Union[ vtkXMLMultiBlockDataReader, vtkXMLUnstructuredGridReader ]
         if datasetType == "multiblock":
-            reader = reader = vtkXMLMultiBlockDataReader()
+            reader = vtkXMLMultiBlockDataReader()
             vtkFilename = "data/displacedFault.vtm"
+        elif datasetType == "emptymultiblock":
+            reader = vtkXMLMultiBlockDataReader()
+            vtkFilename = "data/displacedFaultempty.vtm"
         elif datasetType == "dataset":
-            reader: vtkXMLUnstructuredGridReader = vtkXMLUnstructuredGridReader()
+            reader = vtkXMLUnstructuredGridReader()
             vtkFilename = "data/domain_res5_id.vtu"
+        elif datasetType == "emptydataset":
+            reader = vtkXMLUnstructuredGridReader()
+            vtkFilename = "data/domain_res5_id_empty.vtu"
         elif datasetType == "polydata":
-            reader: vtkXMLUnstructuredGridReader = vtkXMLUnstructuredGridReader()
+            reader = vtkXMLUnstructuredGridReader()
             vtkFilename = "data/surface.vtu"
+
         datapath: str = os.path.join( os.path.dirname( os.path.realpath( __file__ ) ), vtkFilename )
         reader.SetFileName( datapath )
         reader.Update()
 
         return reader.GetOutput()
 
-    return _get_dataset
+    return _get_dataset

geos-mesh/tests/data/displacedFaultempty.vtm

@@ -0,0 +1,7 @@
+<?xml version="1.0"?>
+<VTKFile type="vtkMultiBlockDataSet" version="1.0">
+    <vtkMultiBlockDataSet>
+        <DataSet name="main" file="domain_res5_id_empty.vtu"/>
+        <DataSet name="fracture" file="fracture_res5_id_empty.vtu"/>
+    </vtkMultiBlockDataSet>
+</VTKFile>

geos-mesh/tests/data/fracture_res5_id_empty.vtu

@@ -0,0 +1,41 @@
+<?xml version="1.0"?>
+<VTKFile type="UnstructuredGrid" version="0.1" byte_order="LittleEndian" header_type="UInt32" compressor="vtkZLibDataCompressor">
+  <UnstructuredGrid>
+    <Piece NumberOfPoints="212" NumberOfCells="156">
+      <PointData GlobalIds="GLOBAL_IDS_POINTS">
+        <DataArray type="Int64" IdType="1" Name="GLOBAL_IDS_POINTS" format="binary" RangeMin="0" RangeMax="211">
+          AQAAAACAAACgBgAAbgEAAA==eJwtxdciEAAAAEBRUmlpK9q0aEpbey/tTUMb0d57T6VBO+2NSGjvoflDHrp7uYCA/6o40EGu6moOdnWHuIZrupZDXdt1XNf1XN9hbuCGbuTGbuKmbuZwN3cLRzjSLd3Krd3Gbd3O7R3laHdwR3dyZ3dxjGPd1d3c3T3c070c596Odx/3dT/39wAP9CAneLCHeKiHebhHeKRHebTHeKzHebwneKInebITPcVTPc3TPcMzPcuzPcdzPc/zvcBJTvZCL/JiL3GKl3qZl3uFV3qVVzvVaU73Gmc402u9zuu9wRu9yZu9xVu9zdu9wzu9y7u9x3u9z/t9wAd9yId9xEd9zMd9wid9ylk+7TPO9lmf83lfcI5zfdGXfNlXfNXXfN03nOebvuXbvuO7vuf7fuCHfuTHfuKnzneBC/3MRS72c5f4hUtd5nK/9Cu/9hu/9Tu/9wd/9Cd/9hd/9Td/9w9X+Kd/+bf/+K//uRLqf1df
+        </DataArray>
+      </PointData>
+      <CellData GlobalIds="GLOBAL_IDS_CELLS">
+        <DataArray type="Int64" IdType="1" Name="GLOBAL_IDS_CELLS" format="binary" RangeMin="0" RangeMax="155">
+          AQAAAACAAADgBAAAEgEAAA==eJwtxddCCAAAAMAiozSkoaGh0NAeqGhrSNEg7SFkJKFhlIhoaCBUP9tDdy8XEHAo0Ed81EE+5uM+4ZMOdohPOdRhDneETzvSZxzlaMc41mcd53gnONHnnORkpzjV553mdF/wRV9yhjOd5Wxfdo5zned8F7jQRS52iUt9xVd9zWUud4Wv+4YrXeVq17jWda73TTe40U1u9i23+LZb3eY7vut2d7jTXb7n++72A/e4133u94AHPeRhj3jUDz3mR37sJx73Uz/zc7/whF960q885dd+47ee9oxnPed3fu8P/uh5L/iTF/3ZX7zkr/7mZX/3D6941Wte909veNNb3vYv//Yf7/iv//m/d73nfR8ARZMvOw==
+        </DataArray>
+      </CellData>
+      <Points>
+        <DataArray type="Float32" Name="Points" NumberOfComponents="3" format="binary" RangeMin="0" RangeMax="2304.886114323222">
+          AQAAAACAAADwCQAAXQIAAA==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
+          <InformationKey name="L2_NORM_RANGE" location="vtkDataArray" length="2">
+            <Value index="0">
+              0
+            </Value>
+            <Value index="1">
+              2304.8861143
+            </Value>
+          </InformationKey>
+        </DataArray>
+      </Points>
+      <Cells>
+        <DataArray type="Int64" Name="connectivity" format="binary" RangeMin="0" RangeMax="211">
+          AQAAAACAAACAEwAAWQMAAA==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
+        </DataArray>
+        <DataArray type="Int64" Name="offsets" format="binary" RangeMin="4" RangeMax="624">
+          AQAAAACAAADgBAAADgEAAA==eJwtxRFwAgAAAMC2C4IgCIIgCIIgCIIgCIIgCIIgCIIgCIIgCIIgCIIgCIIgCAaDwSAIgiAIgiAIBkEQDPqXDwbeQg474qhjjjvhpFNOO+Osc8674KJLLrviqmuuu+GmW26746577nvgoUcee+KpZ5574aVXXnvjrb/87R//eue9Dz765LMvvvrmu//88NMvBz7eBR1y2BFHHXPcCSedctoZZ51z3gUXXXLZFVddc90NN91y2x133XPfAw898tgTTz3z3AsvvfLaG2/95W//+Nc7733w0SefffHVN9/954effjnw+S7okMOOOOqY40446ZTTzjjrnPMuuOiSy6646prrbrjpltvu+B9fwUXT
+        </DataArray>
+        <DataArray type="UInt8" Name="types" format="binary" RangeMin="7" RangeMax="7">
+          AQAAAACAAACcAAAADAAAAA==eJxjZx+8AABPhQRF
+        </DataArray>
+      </Cells>
+    </Piece>
+  </UnstructuredGrid>
+</VTKFile>

geos-mesh/tests/test_arrayHelpers.py

@@ -81,6 +81,22 @@ def test_isAttributeInObjectDataSet( dataSetTest: vtkDataSet, attributeName: str
     assert obtained == expected
 
 
+@pytest.mark.parametrize( "attributeName, onpoints, expected", [
+    ( "PORO", False, False ),
+    ( "GLOBAL_IDS_POINTS", True, True ),
+] )
+def test_isAttributeGlobal(
+    dataSetTest: vtkMultiBlockDataSet,
+    attributeName: str,
+    onpoints: bool,
+    expected: bool,
+) -> None:
+    """Test if the attribute is global or partial."""
+    multiBlockDataset: vtkMultiBlockDataSet = dataSetTest( "multiblock" )
+    obtained: bool = arrayHelpers.isAttributeGlobal( multiBlockDataset, attributeName, onpoints )
+    assert obtained == expected
+
+
 @pytest.mark.parametrize( "arrayExpected, onpoints", [
     ( "PORO", False ),
     ( "PERM", False ),
@@ -100,6 +116,35 @@ def test_getArrayInObject( request: pytest.FixtureRequest, arrayExpected: npt.ND
     assert ( obtained == expected ).all()
 
 
+@pytest.mark.parametrize( "attributeName, vtkDataType, onPoints", [
+    ( "CellAttribute", 11, False ),
+    ( "PointAttribute", 11, True ),
+    ( "collocated_nodes", 12, True ),
+] )
+def test_getVtkArrayTypeInMultiBlock( dataSetTest: vtkMultiBlockDataSet, attributeName: str, vtkDataType: int,
+                                      onPoints: bool ) -> None:
+    """Test getting the type of the vtk array of an attribute from multiBlockDataSet."""
+    multiBlockDataSet: vtkMultiBlockDataSet = dataSetTest( "multiblock" )
+
+    vtkDataTypeTest: int = arrayHelpers.getVtkArrayTypeInMultiBlock( multiBlockDataSet, attributeName, onPoints )
+
+    assert ( vtkDataTypeTest == vtkDataType )
+
+
+@pytest.mark.parametrize( "attributeName, onPoints", [
+    ( "CellAttribute", False ),
+    ( "PointAttribute", True ),
+] )
+def test_getVtkArrayTypeInObject( dataSetTest: vtkDataSet, attributeName: str, onPoints: bool ) -> None:
+    """Test getting the type of the vtk array of an attribute from dataset."""
+    vtkDataSetTest: vtkDataSet = dataSetTest( "dataset" )
+
+    obtained: int = arrayHelpers.getVtkArrayTypeInObject( vtkDataSetTest, attributeName, onPoints )
+    expected: int = 11
+
+    assert ( obtained == expected )
+
+
 @pytest.mark.parametrize( "arrayExpected, onpoints", [
     ( "PORO", False ),
     ( "PointAttribute", True ),