Pre/Post deep learning

Some deep learning workflows applied to physics contexts require the projection of fields defined on an unstructured mesh onto a rectilinear grid, and inversely.

Includes

import pyvista
pyvista.global_theme._jupyter_backend = 'panel' # remove this line to get interactive 3D plots
import numpy as np
from Muscat.Bridges.PyVistaBridge import PlotMesh, MeshToPyVista
from Muscat.Helpers.IO.TemporaryDirectory import TemporaryDirectory

PREPROCESSING

Read the solution generated by a physical code

from Muscat.IO import XdmfReader as XR
reader = XR.XdmfReader(filename = "PrePostDeepLearning_Input.xmf")
reader.Read()
grid = reader.xdmf.GetDomain(0).GetGrid(0)

# Read the mesh
uMesh = grid.GetSupport()

# Read the solution field 'U'
indexU = grid.GetPointFieldsNames().index("U")
U = grid.GetPointFields()[indexU][:,0:2]
uMesh.nodeFields["U"] = U
PlotMesh(uMesh,scalars="U", show_edges=True, cpos="xy", show_scalar_bar=False)

Create a rectilinear mesh of size 48*48 excluding the left part of the mesh (x<0)

Nx = 48
Ny = 48
boundingMin, boundingMax = uMesh.ComputeBoundingBox()
Lx = boundingMax[0] - 0.
Ly = boundingMax[1] - boundingMin[1]

from Muscat.Containers.ConstantRectilinearMeshTools import CreateConstantRectilinearMesh
unstructuredRectMesh = CreateConstantRectilinearMesh(dimensions=[Nx,Ny], spacing=[Lx/(Nx-1), Ly/(Ny-1)], origin=[0., boundingMin[1]])
PlotMesh(unstructuredRectMesh, show_edges=True, cpos="xy")

Compute the projection operator from unstructured mesh to structured mesh

from Muscat.FE.FETools import PrepareFEComputation
from Muscat.Containers.MeshFieldOperations import GetFieldTransferOp
from Muscat.FE.Fields.FEField import FEField

inputFEField = FEField(name="U",mesh=uMesh)

operator, status, entities  = GetFieldTransferOp(inputFEField, unstructuredRectMesh.nodes, method = "Interp/Clamp", verbose=True)

# Compute the projected field on the structured mesh
projectedU = operator.dot(U)

unstructuredRectMesh.nodeFields["projectedU"] = projectedU
PlotMesh(unstructuredRectMesh,scalars="projectedU", show_edges=True, cpos="xy", show_scalar_bar=False)

Starting C++ FieldTransfer
Done c++ FieldTransfer

Export the structured mesh and projected field in xdmf format (in ASCII)

# To visualize this xdmf file you can use ParaView (downloadable from https://www.paraview.org/)
from Muscat.IO import XdmfWriter as XW
writer = XW.XdmfWriter(TemporaryDirectory.GetTempPath() + 'PrePostDeepLearning_OutputI.xdmf')
writer.SetHdf5(False)
writer.Open()
writer.Write(unstructuredRectMesh,PointFields=[projectedU], PointFieldsNames=["U"])
writer.Close()

POSTPROCESSING

# Compute the projection operator from the structured mesh to the unstructured mesh (inverse projection)
inputFEField = FEField(name="U",mesh=unstructuredRectMesh)
operator, status, entities = GetFieldTransferOp(inputFEField, uMesh.nodes, method =  "Interp/Clamp", verbose=True)

# Compute the inverse-projected projected field on the unstructured mesh
inverseProjected_ProjectedU = operator.dot(projectedU)

uMesh.nodeFields["inverseProjected_ProjectedU"] = inverseProjected_ProjectedU
PlotMesh(uMesh,scalars="inverseProjected_ProjectedU", show_edges=False, cpos="xy", show_scalar_bar=False)

Starting C++ FieldTransfer
Done c++ FieldTransfer

CHECK ACCURACY

# Create a clippedMesh from the unstructured mesh by removing the left part (x<0)
# (with field, inverse-projected projected field and difference between them)
from Muscat.Containers.Filters.FilterObjects import ElementFilter
from Muscat.FE.FETools import ComputePhiAtIntegPoint, ComputeL2ScalarProductMatrix
from Muscat.Containers.MeshInspectionTools import ExtractElementsByElementFilter
from Muscat.Containers.MeshModificationTools import CleanLonelyNodes
from Muscat.Containers.MeshFieldOperations import CopyFieldsFromOriginalMeshToTargetMesh

uMesh.nodeFields['delta'] = U - inverseProjected_ProjectedU

elFilter = ElementFilter(zone = lambda p: (-p[:,0]))
meshClipped = ExtractElementsByElementFilter(uMesh, elFilter)
CleanLonelyNodes(meshClipped)

CopyFieldsFromOriginalMeshToTargetMesh(uMesh, meshClipped)
nbeOfNodes = meshClipped.GetNumberOfNodes()

deltaClippedMesh = meshClipped.nodeFields['delta']

PlotMesh(meshClipped,scalars="delta", show_edges=False, cpos="xy", show_scalar_bar=True)

Computetion of the integral of the delta

from Muscat.Helpers.TextFormatHelper import TFormat
from Muscat.Helpers.Timer import Timer

print("Compute the L2(Omega) norm of delta by applying numerical quadrature from Lagrange P1")
print("Finite element integration using three different methods")

#### Method 1 #######################################################################################################################
print(TFormat.Center(TFormat.InRed("Method 1: ")+TFormat.InBlue("'by hand'")))

timer = Timer("Duration of method 1")
#compute method 1 three times
for i in range(2):
    timer.Start()
    integrationWeights, phiAtIntegPoint = ComputePhiAtIntegPoint(meshClipped)

    vectDeltaAtIntegPoints = np.empty((2,phiAtIntegPoint.shape[0]))
    for i in range(2):
        vectDeltaAtIntegPoints[i] = phiAtIntegPoint.dot(deltaClippedMesh[:,i])

    normDeltaMethod1 = np.sqrt(np.einsum('ij,ij,j', vectDeltaAtIntegPoints, vectDeltaAtIntegPoints, integrationWeights, optimize = True))
    timer.Stop()

print("norm(Delta) =", normDeltaMethod1)
############
#### Method 2 #######################################################################################################################
print(TFormat.Center(TFormat.InRed("Method 2: ")+TFormat.InBlue("using the mass matrix")))

timer = Timer("Duration of method 2").Start()

massMatrix = ComputeL2ScalarProductMatrix(meshClipped, 2)

normDeltaMethod2 = np.sqrt(np.dot(deltaClippedMesh.ravel(order='F'), massMatrix.dot(deltaClippedMesh.ravel(order='F'))))

timer.Stop()
print("norm(Delta) =", normDeltaMethod2)

#### Method 3 #######################################################################################################################
print(TFormat.Center(TFormat.InRed("Method 3: ")+TFormat.InBlue("using Muscat integration tool")))

from Muscat.FE.IntegrationTools import IntegrateField
timer = Timer("Duration of method 3").Start()
deltaSquare_U0 = FEField("delta_U0",meshClipped,data= deltaClippedMesh[:,0].flatten() )**2 + FEField("delta_U1",meshClipped,data= deltaClippedMesh[:,1].flatten() )**2
F = IntegrateField(deltaSquare_U0, ElementFilter(dimensionality=2))
timer.Stop()
print("norm(Delta) =", np.sqrt(F))

#### Method 4 #######################################################################################################################
print(TFormat.Center(TFormat.InRed("Method 3: ")+TFormat.InBlue("using the weak form engine")))

from Muscat.FE.Integration import IntegrateGeneral
from Muscat.FE.SymWeakForm import GetField, GetTestField
from Muscat.FE.Spaces.FESpaces import LagrangeSpaceP1, ConstantSpaceGlobal
from Muscat.FE.DofNumbering import ComputeDofNumbering

timer = Timer("Duration of method 4").Start()

U = GetField("U",2)
Tt = GetTestField("T",1)

wf = U.T*U*Tt

#meshClipped

field1 = FEField("U_0",mesh=meshClipped, data = deltaClippedMesh[:,0].flatten())
field2 = FEField("U_1",mesh=meshClipped, data = deltaClippedMesh[:,1].flatten())

numbering = ComputeDofNumbering(meshClipped,ConstantSpaceGlobal)
unknownField = FEField("T",mesh=meshClipped,space=ConstantSpaceGlobal,numbering=numbering)

elFilter = ElementFilter()

K, F = IntegrateGeneral(mesh=meshClipped,
                    wform=wf,
                    constants={},
                    fields=[field1,field2],
                    unknownFields=[unknownField],
                    integrationRuleName="LagrangeP1Quadrature",
                    elementFilter=elFilter)

normDeltaMethod3 = np.sqrt(F[0])

timer.Stop()
print("norm(Delta) =", normDeltaMethod2)
############

print(Timer.PrintTimes())

Compute the L2(Omega) norm of delta by applying numerical quadrature from Lagrange P1
Finite element integration using three different methods
******************** Method 1: 'by hand' *******************
norm(Delta) = 0.0001466583268059577
************** Method 2: using the mass matrix *************
norm(Delta) = 0.00014665832680595773
********** Method 3: using Muscat integration tool *********
norm(Delta) = 0.0001555718367085269
*********** Method 3: using the weak form engine ***********
norm(Delta) = 0.00014665832680595773

Duration of method 1:   (2) : 6.293e+00 s (mean 3.147e+00 s/call)
Duration of method 2:   (1) : 3.520e-02 s (mean 3.520e-02 s/call)
Duration of method 3:   (1) : 3.619e-01 s (mean 3.619e-01 s/call)
Duration of method 4:   (1) : 1.984e-02 s (mean 1.984e-02 s/call)