Commit 1b5f8273 authored by Felipe Bordeu's avatar Felipe Bordeu Committed by Felipe Bordeu
Browse files

(vtkBridge.py) source reformatting

parent 36d799d9

src/BasicTools/Bridges/vtkBridge.py

+244 −215
Original line number Diff line number Diff line
@@ -13,7 +13,7 @@ try: 
except:

    try:

        # faster import only needed classes

        from vtkmodules.vtkCommonCore import vtkPoints, vtkIdList#, vtkUnsignedCharArray, , vtkIdTypeArray

        from vtkmodules.vtkCommonCore import vtkPoints, vtkIdList

        from vtkmodules.vtkCommonDataModel import vtkPolyData, vtkUnstructuredGrid, vtkImageData, vtkCellArray

        from vtkmodules.util import numpy_support

    except:
@@ -129,12 +129,14 @@ elementNameByVtkNumber[11] = ElementNames.Hexaedron_8 #voxel 
# converted to a tag. the first type is used to encode tags in vtk

tagsTypes = [np.int8, np.uint8, int]





def VtkFieldToNumpyField(support: UnstructuredMesh, vtkField) -> np.ndarray:

    if support.IsConstantRectilinear():

        return VtkFieldToNumpyFieldWithDims(vtkField, dimensions=support.GetDimensions())

    else:

        return VtkFieldToNumpyFieldWithDims(vtkField)





def VtkFieldToNumpyFieldWithDims(vtkField, dimensions=None):

    from vtkmodules.util import numpy_support

    from vtkmodules.vtkCommonCore import vtkStringArray
@@ -158,12 +160,14 @@ def VtkFieldToNumpyFieldWithDims(vtkField,dimensions=None): 


    return (name, data)





def NumpyFieldToVtkField(support: UnstructuredMesh, fieldData: ArrayLike, fieldName: str):

    if support.IsConstantRectilinear():

        return NumpyFieldToVtkFieldWithDims(fieldData, fieldName, support.GetDimensions())

    else:

        return NumpyFieldToVtkFieldWithDims(fieldData, fieldName)





def NumpyFieldToVtkFieldWithDims(fieldData: ArrayLike, fieldName: str, dimensions=None):

    from vtkmodules.util import numpy_support

    from vtkmodules.vtkCommonCore import vtkStringArray
@@ -192,7 +196,8 @@ def NumpyFieldToVtkFieldWithDims(fieldData: ArrayLike, fieldName: str, dimension 
                dims = newshape

            dims.append(fieldData.shape[1])

            dataView.shape = tuple(dims)

          VTK_data = numpy_support.numpy_to_vtk(num_array=np.swapaxes(dataView,0,2).ravel(), deep=True, array_type=outputtype)

            VTK_data = numpy_support.numpy_to_vtk(num_array=np.swapaxes(

                dataView, 0, 2).ravel(), deep=True, array_type=outputtype)

        else:

            VTK_data = numpy_support.numpy_to_vtk(num_array=fieldData, deep=True, array_type=outputtype)

        VTK_data.SetNumberOfComponents(fieldData.shape[1])
@@ -208,17 +213,20 @@ def NumpyFieldToVtkFieldWithDims(fieldData: ArrayLike, fieldName: str, dimension 
                # elemfield

                newshape = tuple([(x-1 if x-1 > 0 else 1) for x in dimensions])

                dataView.shape = newshape

          VTK_data = numpy_support.numpy_to_vtk(num_array=np.swapaxes(dataView,0,2).ravel(), deep=True, array_type=outputtype)

            VTK_data = numpy_support.numpy_to_vtk(num_array=np.swapaxes(

                dataView, 0, 2).ravel(), deep=True, array_type=outputtype)

        else:

            VTK_data = numpy_support.numpy_to_vtk(num_array=fieldData, deep=True, array_type=outputtype)

    VTK_data.SetName(fieldName)

    return VTK_data





def ApplyVtkPipeline(mesh: UnstructuredMesh, op: Callable) -> UnstructuredMesh:

    vtkMesh = MeshToVtk(mesh)

    vtkOutputMesh = op(vtkMesh)

    return VtkToMesh(vtkOutputMesh)





def PlotMesh(mesh):  # pragma: no cover

    from vtkmodules.vtkFiltersGeometry import vtkGeometryFilter

    from vtkmodules.vtkRenderingCore import vtkPolyDataMapper, vtkActor, vtkRenderer, vtkRenderWindow, vtkRenderWindowInteractor, vtkColorTransferFunction
@@ -230,7 +238,6 @@ def PlotMesh(mesh):# pragma: no cover 
    import vtkmodules.vtkRenderingOpenGL2

    import vtkmodules.vtkRenderingFreeType





    from BasicTools.Containers.MeshBase import MeshBase



    if isinstance(mesh, MeshBase):
@@ -325,7 +332,7 @@ def PlotMesh(mesh):# pragma: no cover 
    buttonWidget.AddObserver('StateChangedEvent', listener.processStateChangeEvent)



    buttonRepresentation = vtkTexturedButtonRepresentation2D()

    buttonRepresentation.SetNumberOfStates(1);

    buttonRepresentation.SetNumberOfStates(1)

    r = vtkPNGReader()



    fileName = GetTestDataPath()+"Next.png"
@@ -340,7 +347,7 @@ def PlotMesh(mesh):# pragma: no cover 


    buttonWidget.SetRepresentation(buttonRepresentation)



    buttonWidget.On();

    buttonWidget.On()



    iren.Initialize()
@@ -359,8 +366,8 @@ def PlotMesh(mesh):# pragma: no cover 
    iren.TerminateApp()

    del renWin, iren



def MeshToVtk(mesh, vtkobject=None, TagsAsFields=False):



def MeshToVtk(mesh, vtkobject=None, TagsAsFields=False):



    # From www.vtk;org/wp-content/updloads/2015/04/file-formats.pdf
@@ -398,7 +405,7 @@ def MeshToVtk(mesh, vtkobject=None, TagsAsFields=False): 
            return output



        output.Allocate(mesh.GetNumberOfElements())

        ##copy points

        # copy points



        VTK_originalIDNodes = NumpyFieldToVtkField(mesh, mesh.originalIDNodes, "originalIds")

        output.GetPointData().AddArray(VTK_originalIDNodes)
@@ -426,7 +433,8 @@ def MeshToVtk(mesh, vtkobject=None, TagsAsFields=False): 
                nbElement = elementContainer.GetNumberOfElements()



                cellTypes[cpt:cpt+nbElement] = vtkNumberByElementName[elementsName]

                offsets[cpt:cpt+nbElement] = offsetcpt + np.arange(nbElement)*elementContainer.GetNumberOfNodesPerElement()

                offsets[cpt:cpt+nbElement] = offsetcpt + \

                    np.arange(nbElement)*elementContainer.GetNumberOfNodesPerElement()



                offsetcpt += elementContainer.GetNumberOfNodesPerElement()*nbElement

                cpt += nbElement
@@ -441,7 +449,6 @@ def MeshToVtk(mesh, vtkobject=None, TagsAsFields=False): 
                connectivity[offsetcpt:offsetcpt+nbObjects] = elementContainer.connectivity.flatten()

                offsetcpt += nbObjects





            offsets = numpy_support.numpy_to_vtkIdTypeArray(offsets, deep=True)

            connectivity = numpy_support.numpy_to_vtkIdTypeArray(connectivity, deep=True)
@@ -465,8 +472,10 @@ def MeshToVtk(mesh, vtkobject=None, TagsAsFields=False): 
            if data is None:  # pragma: no cover

                continue

            if np.size(data)//mesh.GetNumberOfNodes() != np.size(data)/mesh.GetNumberOfNodes():

                print("field ("+str(name)+") is not consistent : it has " + str(np.size(data)) +" values and the mesh has " +str(mesh.GetNumberOfNodes())+ " nodes" )

                raise Exception("field ("+str(name)+") is not consistent : it has " + str(np.size(data)) +" values and the mesh has " +str(mesh.GetNumberOfNodes())+ " nodes" )

                print("field ("+str(name)+") is not consistent : it has " + str(np.size(data)) +

                      " values and the mesh has " + str(mesh.GetNumberOfNodes()) + " nodes")

                raise Exception("field ("+str(name)+") is not consistent : it has " + str(np.size(data)

                                                                                          ) + " values and the mesh has " + str(mesh.GetNumberOfNodes()) + " nodes")



            VTK_data = NumpyFieldToVtkField(mesh, data, name)

            output.GetPointData().AddArray(VTK_data)
@@ -491,7 +500,8 @@ def MeshToVtk(mesh, vtkobject=None, TagsAsFields=False): 
                continue



            if np.size(data)/mesh.GetNumberOfElements() != np.size(data)//mesh.GetNumberOfElements():  # pragma: no cover

                print("field ("+str(name)+") is not consistent : it has " + str(np.size(data)) +" values and the mesh has " +str(mesh.GetNumberOfElements())+ " elements" )

                print("field ("+str(name)+") is not consistent : it has " + str(np.size(data)) +

                      " values and the mesh has " + str(mesh.GetNumberOfElements()) + " elements")

                continue



            VTK_data = NumpyFieldToVtkField(mesh, data, name)
@@ -510,6 +520,7 @@ def MeshToVtk(mesh, vtkobject=None, TagsAsFields=False): 


    return output





def VtkToMeshOnlyMeta(vtkmesh, FieldsAsTags=False):

    from vtkmodules.util import numpy_support
@@ -576,8 +587,8 @@ def VtkToMeshOnlyMeta(vtkmesh, FieldsAsTags=False): 
                res.nodeFields.append(name)

    return res



def AddCellsFromVtkCellArrayToMesh(cells, cellTypesArray:ArrayLike, out:UnstructuredMesh, originalIdsOffset=0):



def AddCellsFromVtkCellArrayToMesh(cells, cellTypesArray: ArrayLike, out: UnstructuredMesh, originalIdsOffset=0):

    """Function to migrate cells from a vtkCellArray to a BasicTools Unstructured Mesh



    Parameters
@@ -614,7 +625,8 @@ def AddCellsFromVtkCellArrayToMesh(cells, cellTypesArray:ArrayLike, out:Unstruct 
        nbNewElements = len(index)

        cpt1 = cpt0+nbNewElements



        mask=np.arange(numberOfNodesPerElement, dtype=PBasicIndexType)*np.ones((len(index),numberOfNodesPerElement), dtype=PBasicIndexType)+offsets[index,None]

        mask = np.arange(numberOfNodesPerElement, dtype=PBasicIndexType) * \

            np.ones((len(index), numberOfNodesPerElement), dtype=PBasicIndexType)+offsets[index, None]

        localConnectivity = connectivity[mask]

        localConnectivity.shape = (nbNewElements, numberOfNodesPerElement)

        elements.connectivity[cpt0:cpt1, :] = localConnectivity
@@ -630,6 +642,7 @@ def AddCellsFromVtkCellArrayToMesh(cells, cellTypesArray:ArrayLike, out:Unstruct 


    return nbNewElements





def VtkToMesh(vtkmesh, meshobject=None, FieldsAsTags=True):



    if meshobject is None:
@@ -674,7 +687,6 @@ def VtkToMesh(vtkmesh, meshobject=None, FieldsAsTags=True): 
        out.originalIDNodes = None

        AddCellsFromVtkCellArrayToMesh(vtkmesh.GetCells(), vtkmesh.GetCellTypesArray(), out)





    if vtkmesh.GetPointData().GetNumberOfArrays():

        for f in range(vtkmesh.GetPointData().GetNumberOfArrays()):

            data = vtkmesh.GetPointData().GetArray(f)
@@ -720,6 +732,7 @@ def VtkToMesh(vtkmesh, meshobject=None, FieldsAsTags=True): 


    return out





def GetInputVtk(request, inInfoVec, outInfoVec, port=0):

    from vtkmodules.vtkCommonDataModel import vtkUnstructuredGrid, vtkPolyData

    input0 = vtkUnstructuredGrid.GetData(inInfoVec[port])
@@ -727,10 +740,12 @@ def GetInputVtk(request, inInfoVec, outInfoVec, port=0): 
        input0 = vtkPolyData.GetData(inInfoVec[port])

    return input0





def GetInputBasicTools(request, inInfoVec, outInfoVec, FieldsAsTags=False, port=0):

    vtkobj = GetInputVtk(request, inInfoVec, outInfoVec, port=port)

    return VtkToMesh(vtkobj, FieldsAsTags=FieldsAsTags)





def GetOutputVtk(request, inInfoVec, outInfoVec, copyAttr=True, outputNumber=0):

    from vtkmodules.vtkCommonDataModel import vtkUnstructuredGrid

    output = vtkUnstructuredGrid.GetData(outInfoVec, outputNumber)
@@ -739,10 +754,12 @@ def GetOutputVtk(request, inInfoVec, outInfoVec, copyAttr = True, outputNumber= 
        output.CopyAttributes(input0)

    return output





def SetOutputBasicTools(request, inInfoVec, outInfoVec, outMesh, TagsAsFields=False):

    output = GetOutputVtk(request, inInfoVec, outInfoVec, False)

    MeshToVtk(outMesh, output, TagsAsFields=TagsAsFields)





def VtkToMeshMultiblock(vtkObject, OP=VtkToMesh):

    if input.IsA("vtkMultiBlockDataSet"):

        res = list()
@@ -753,6 +770,7 @@ def VtkToMeshMultiblock(vtkObject,OP=VtkToMesh): 
    else:

        return OP(input)





def CellDataToPoint(mesh: UnstructuredMesh, cellfields: np.ndarray) -> np.ndarray:

    """Applies the CellDataToPointData from vtk.

    Supported only for the dimensionality of the mesh (no mix of elements of different
@@ -790,12 +808,14 @@ def CellDataToPoint(mesh:UnstructuredMesh, cellfields:np.ndarray) -> np.ndarray: 


    return np.array(res)





def ReadMeshAndPopulateVtkObject(filename, vtkobject=None, TagsAsFields=False):  # pragma: no cover

    from BasicTools.IO.UniversalReader import ReadMesh as UReadMesh

    mesh = UReadMesh(filename)

    from BasicTools.Bridges.vtkBridge import MeshToVtk

    return MeshToVtk(mesh, vtkobject, TagsAsFields=TagsAsFields)





def CheckIntegrity_VtkToMesh(GUI=False):

    from BasicTools.Containers.UnstructuredMeshCreationTools import CreateMeshOf

    points = [[0, 0, 0], [1, 0, 0], [0, 1, 0], [0, 0, 1]]
@@ -803,7 +823,8 @@ def CheckIntegrity_VtkToMesh(GUI=False): 
    res = CreateMeshOf(points, tet, elemName=ElementNames.Tetrahedron_4)

    res.nodeFields = {"x": res.nodes[:, 0].flatten(), "Pos": res.nodes}

    res.nodesTags.CreateTag("FirstPoint").AddToTag(0)

    res.elemFields = {"SecondPoint": res.GetElementsOfType(ElementNames.Tetrahedron_4).connectivity[:,1].flatten().astype(float), "conn": res.GetElementsOfType(ElementNames.Tetrahedron_4).connectivity }

    res.elemFields = {"SecondPoint": res.GetElementsOfType(ElementNames.Tetrahedron_4).connectivity[:, 1].flatten().astype(

        float), "conn": res.GetElementsOfType(ElementNames.Tetrahedron_4).connectivity}

    res.GetElementsOfType(ElementNames.Tetrahedron_4).tags.CreateTag("FirstTetrahedron").AddToTag(0)

    sol = MeshToVtk(res, TagsAsFields=True)
@@ -820,12 +841,14 @@ def CheckIntegrity_VtkToMesh(GUI=False): 
        raise (Exception("The meshes are not equal"))

    return 'ok'





def CheckIntegrity_VtkToMesh2D(GUI=False):

    res = CreateMeshOfTriangles([[0, 0], [1, 0], [1, 1], [1, 1]], [[0, 1, 2], [0, 2, 3]])



    res.nodeFields = {"x": res.nodes[:, 0].flatten(), "Pos": res.nodes}

    res.nodesTags.CreateTag("FirstPoint").AddToTag(0)

    res.elemFields = {"SecondPoint": res.GetElementsOfType(ElementNames.Triangle_3).connectivity[:,1].flatten().astype(float), "conn": res.GetElementsOfType(ElementNames.Triangle_3).connectivity }

    res.elemFields = {"SecondPoint": res.GetElementsOfType(ElementNames.Triangle_3).connectivity[:, 1].flatten().astype(

        float), "conn": res.GetElementsOfType(ElementNames.Triangle_3).connectivity}

    res.GetElementsOfType(ElementNames.Triangle_3).tags.CreateTag("FirstTriangle").AddToTag(0)

    sol = MeshToVtk(res, TagsAsFields=True)
@@ -847,7 +870,8 @@ def CheckIntegrity_MeshToVtk(GUI=False): 
    res = CreateMeshOfTriangles([[0, 0, 0], [1, 0, 0], [0, 1, 0], [0, 0, 1]], [[0, 1, 2], [0, 2, 3]])

    res.nodeFields = {"x": res.nodes[:, 0].flatten(), "Pos": res.nodes}

    res.nodesTags.CreateTag("FirstPoint").AddToTag(0)

    res.elemFields = {"SecondPoint": res.GetElementsOfType(ElementNames.Triangle_3).connectivity[:,1].flatten(), "conn": res.GetElementsOfType(ElementNames.Triangle_3).connectivity, "FE Names":np.array(['c2d3','c2d3'],dtype=np.str_) }

    res.elemFields = {"SecondPoint": res.GetElementsOfType(ElementNames.Triangle_3).connectivity[:, 1].flatten(

    ), "conn": res.GetElementsOfType(ElementNames.Triangle_3).connectivity, "FE Names": np.array(['c2d3', 'c2d3'], dtype=np.str_)}

    res.GetElementsOfType(ElementNames.Triangle_3).tags.CreateTag("FirstTriangle").AddToTag(0)

    sol = MeshToVtk(res, TagsAsFields=True)

    print(sol)
@@ -856,7 +880,7 @@ def CheckIntegrity_MeshToVtk(GUI=False): 
    if not IsClose(res, resII):  # pragma: no cover

        raise (Exception("The meshes are not equal"))



    ## test a 2D mesh

    # test a 2D mesh

    res = CreateMeshOfTriangles([[0, 0], [1, 0], [0, 1], [1, 1]], [[0, 1, 2], [2, 1, 3]])

    if GUI:  # pragma: no cover

        res.nodeFields["Field1"] = np.array([30, 20, 30, 1])
@@ -868,6 +892,7 @@ def CheckIntegrity_MeshToVtk(GUI=False): 


    return "OK"





def CheckIntegrity_ConstantRectilinearMesh(GUI=False):

    print("*** CheckIntegrity_ConstantRectilinearMesh **** ")

    from BasicTools.Containers.ConstantRectilinearMeshTools import CreateMesh
@@ -888,8 +913,10 @@ def CheckIntegrity_ConstantRectilinearMesh(GUI=False): 
    if not IsClose(crm, crmII):  # pragma: no cover

        raise (Exception("The meshes are not equal"))





def checkIntegrity_ApplyVtkPipeline(GUI):

    res = CreateMeshOfTriangles([[0, 0, 0], [1, 0, 0], [0, 1, 0], [0, 0, 1]], [[0, 1, 2], [0, 2, 3]])



    class op():

        def __call__(self, vtkinput):

            from vtkmodules.vtkFiltersModeling import vtkLinearExtrusionFilter
@@ -918,6 +945,7 @@ def CheckIntegrity_CellDataToPoint(GUI = False): 
    CellDataToPoint(mesh, cellField)

    return "ok"





def CheckIntegrity(GUI=False):

    try:

        numpy_support
@@ -932,5 +960,6 @@ def CheckIntegrity(GUI=False): 
    CheckIntegrity_CellDataToPoint(GUI)

    return 'ok'





if __name__ == '__main__':

    print(CheckIntegrity(True))  # pragma: no cover