def qualityCompare(self):
meshQuality = vtk.vtkMeshQuality()
meshQuality.SetInputData(self.Mesh)
meshQuality.RatioOn()
meshQuality.Update()
meshQualityOutput = meshQuality.GetOutput()
referenceQuality = vtk.vtkMeshQuality()
referenceQuality.SetInputData(self.ReferenceMesh)
referenceQuality.RatioOn()
referenceQuality.Update()
referenceQualityOutput = referenceQuality.GetOutput()
self.PrintLog("Mesh points: " + str(meshQualityOutput.GetNumberOfPoints()))
self.PrintLog("Reference Points: " + str(referenceQualityOutput.GetNumberOfPoints()))
meshQualityRange = meshQualityOutput.GetCellData().GetArray("Quality").GetRange()
referenceQualityRange = referenceQualityOutput.GetCellData().GetArray("Quality").GetRange()
qualityRangeDifference = (
meshQualityRange[0] - referenceQualityRange[0],
meshQualityRange[1] - referenceQualityRange[1],
)
self.PrintLog("Mesh Quality Range: " + str(meshQualityRange))
self.PrintLog("Reference Quality Range: " + str(referenceQualityRange))
self.PrintLog("Quality Range Difference: " + str(qualityRangeDifference))
if max(abs(d) for d in qualityRangeDifference) < self.Tolerance:
return True
return False
def qualityCompare(self):
meshQuality = vtk.vtkMeshQuality()
meshQuality.SetInputData(self.Mesh)
meshQuality.RatioOn()
meshQuality.Update()
meshQualityOutput = meshQuality.GetOutput()
referenceQuality = vtk.vtkMeshQuality()
referenceQuality.SetInputData(self.ReferenceMesh)
referenceQuality.RatioOn()
referenceQuality.Update()
referenceQualityOutput = referenceQuality.GetOutput()
self.PrintLog("Mesh points: "+ str(meshQualityOutput.GetNumberOfPoints()))
self.PrintLog("Reference Points: " +str(referenceQualityOutput.GetNumberOfPoints()))
meshQualityRange = meshQualityOutput.GetCellData().GetArray("Quality").GetRange()
referenceQualityRange = referenceQualityOutput.GetCellData().GetArray("Quality").GetRange()
qualityRangeDifference = (meshQualityRange[0] - referenceQualityRange[0],meshQualityRange[1] - referenceQualityRange[1])
self.PrintLog("Mesh Quality Range: "+ str(meshQualityRange))
self.PrintLog("Reference Quality Range: "+ str(referenceQualityRange))
self.PrintLog("Quality Range Difference: "+ str(qualityRangeDifference))
if max(abs(d) for d in qualityRangeDifference) < self.Tolerance:
return True
return False
def computePolyQualityMinAngle(polydata):
'''
Returns [ min, average, max, variance, number of cells ] of Minmum included Angleof the polydata's triangles.
Acceptable range = [30°,60°]
for equilateral unit triangle = 60°
reference: Verdict reference manual, Stimpson, 2007
'''
qual = vtk.vtkMeshQuality()
qual.SetInput(polydata)
qual.VolumeOn()
qual.RatioOn()
qual.SetTriangleQualityMeasureToMinAngle()
qual.Update()
return [
qual.GetOutput().GetFieldData().GetArray(
"Mesh Triangle Quality").GetValue(0),
qual.GetOutput().GetFieldData().GetArray(
"Mesh Triangle Quality").GetValue(1),
qual.GetOutput().GetFieldData().GetArray(
"Mesh Triangle Quality").GetValue(2),
qual.GetOutput().GetFieldData().GetArray(
"Mesh Triangle Quality").GetValue(3),
qual.GetOutput().GetFieldData().GetArray(
"Mesh Triangle Quality").GetValue(4)
]
def computePolyQualityAspectFrobenius(polydata):
'''
Returns [ min, average, max, variance, number of cells ] of Aspect Frobenius of the polydata's triangles.
Aspect Frobenius is defined as q = ( ||L0||^2+||L1||^2+||L2||^2 ) / ( 4*Area*sqrt(3) )
Acceptable range = [1,1.3]
for equilateral unit triangle = 1
reference: Verdict reference manual, Stimpson, 2007
'''
qual = vtk.vtkMeshQuality()
qual.SetInput(polydata)
qual.VolumeOn()
qual.RatioOn()
qual.SetTriangleQualityMeasureToAspectFrobenius()
qual.Update()
return [
qual.GetOutput().GetFieldData().GetArray(
"Mesh Triangle Quality").GetValue(0),
qual.GetOutput().GetFieldData().GetArray(
"Mesh Triangle Quality").GetValue(1),
qual.GetOutput().GetFieldData().GetArray(
"Mesh Triangle Quality").GetValue(2),
qual.GetOutput().GetFieldData().GetArray(
"Mesh Triangle Quality").GetValue(3),
qual.GetOutput().GetFieldData().GetArray(
"Mesh Triangle Quality").GetValue(4)
]
def computePolyQualityRadiusRatio(polydata):
'''
Returns [ min, average, max, variance, number of cells ] of Radius Ratio of the polydata's triangles.
Radius ratio is defined as q = ( R ) / ( 2r )
where R = circumradius ( = L0*L1*L2 / ( 2*r*(L0+L1+L2) ) ) and r = inradius ( r = 2*Area/(L0+L1+L2) )
Acceptable range = [1,1.3]
for equilateral unit triangle = 1
reference: Verdict reference manual, Stimpson, 2007
'''
qual = vtk.vtkMeshQuality()
qual.SetInput(polydata)
qual.VolumeOn()
qual.RatioOn()
qual.SetTriangleQualityMeasureToRadiusRatio()
qual.Update()
return [
qual.GetOutput().GetFieldData().GetArray(
"Mesh Triangle Quality").GetValue(0),
qual.GetOutput().GetFieldData().GetArray(
"Mesh Triangle Quality").GetValue(1),
qual.GetOutput().GetFieldData().GetArray(
"Mesh Triangle Quality").GetValue(2),
qual.GetOutput().GetFieldData().GetArray(
"Mesh Triangle Quality").GetValue(3),
qual.GetOutput().GetFieldData().GetArray(
"Mesh Triangle Quality").GetValue(4)
]
def computePolyQualityAspectRatio(polydata):
'''
Returns [ min, average, max, variance, number of cells ] of aspect ratio of the polydata's triangles.
Aspect Ratio is defined as q = Lmax / ( 2 * sqrt(3) * r ) = Lmax*(L0+L1+L2) / (4*sqrt(3)*Area)
where Lmax = largest edge and r = inradius ( r = 2*Area/(L0+L1+L2) )
Acceptable range = [1,1.3]
for equilateral unit triangle = 1
reference: Verdict reference manual, Stimpson, 2007
'''
qual = vtk.vtkMeshQuality()
qual.SetInput(polydata)
qual.VolumeOn()
qual.RatioOn()
qual.SetTriangleQualityMeasureToAspectRatio()
qual.Update()
return [
qual.GetOutput().GetFieldData().GetArray(
"Mesh Triangle Quality").GetValue(1),
qual.GetOutput().GetFieldData().GetArray(
"Mesh Triangle Quality").GetValue(2), 0,
qual.GetOutput().GetFieldData().GetArray(
"Mesh Triangle Quality").GetValue(3),
qual.GetOutput().GetFieldData().GetArray(
"Mesh Triangle Quality").GetValue(4)
]
def computePolyQualityEdgeRatio(polydata):
'''
Returns [ min, average, max, variance, number of cells ] of edge ratio of the polydata's triangles.
Edge Ratio is defined as q = Lmax / Lmin
where Lmax = largest edge Lmin = smallest edge
Acceptable range = [1,1.3]
for equilateral unit triangle = 1
reference: Verdict reference manual, Stimpson, 2007
'''
qual = vtk.vtkMeshQuality()
qual.SetInput(polydata)
qual.VolumeOn()
qual.RatioOn()
qual.SetTriangleQualityMeasureToAspectRatio()
qual.Update()
return [
qual.GetOutput().GetFieldData().GetArray(
"Mesh Triangle Quality").GetValue(0),
qual.GetOutput().GetFieldData().GetArray(
"Mesh Triangle Quality").GetValue(1),
qual.GetOutput().GetFieldData().GetArray(
"Mesh Triangle Quality").GetValue(2),
qual.GetOutput().GetFieldData().GetArray(
"Mesh Triangle Quality").GetValue(3),
qual.GetOutput().GetFieldData().GetArray(
"Mesh Triangle Quality").GetValue(4)
]
def test_linear_copy_surf_elem():
cells = np.array([8, 0, 1, 2, 3, 4, 5, 6, 7, 6, 8, 9, 10, 11, 12, 13],
np.int32)
celltypes = np.array([vtk.VTK_QUADRATIC_QUAD, vtk.VTK_QUADRATIC_TRIANGLE],
np.uint8)
cell0 = [[0.0, 0.0, 0.0], [1.0, 0.0, 0.0], [1.0, 1.0,
0.0], [0.0, 1.0, 0.0],
[0.5, 0.1, 0.0], [1.1, 0.5, 0.0], [0.5, 0.9, 0.0],
[0.1, 0.5, 0.0]]
cell1 = [[0.0, 0.0, 1.0], [1.0, 0.0, 1.0], [0.5, 0.5, 1.0],
[0.5, 0.0, 1.3], [0.7, 0.7, 1.3], [0.1, 0.1, 1.3]]
points = np.vstack((cell0, cell1))
if VTK9:
grid = pyvista.UnstructuredGrid(cells, celltypes, points, deep=False)
else:
offset = np.array([0, 9])
grid = pyvista.UnstructuredGrid(offset,
cells,
celltypes,
points,
deep=False)
lgrid = grid.linear_copy()
qfilter = vtk.vtkMeshQuality()
qfilter.SetInputData(lgrid)
qfilter.Update()
qual = pyvista.wrap(qfilter.GetOutput())['Quality']
assert np.allclose(qual, [1, 1.4], atol=0.01)
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
vtk.vtkMeshQuality(), 'Processing.',
('vtkDataSet',), ('vtkDataSet',),
replaceDoc=True,
inputFunctions=None, outputFunctions=None)
def __init__(self, parent=None):
super(VTKFrame, self).__init__(parent)
self.vtkWidget = QVTKRenderWindowInteractor(self)
vl = QtGui.QVBoxLayout(self)
vl.addWidget(self.vtkWidget)
vl.setContentsMargins(0, 0, 0, 0)
self.ren = vtk.vtkRenderer()
self.ren.SetBackground(0.1, 0.2, 0.4)
self.vtkWidget.GetRenderWindow().AddRenderer(self.ren)
self.iren = self.vtkWidget.GetRenderWindow().GetInteractor()
# Create source
source = vtk.vtkSphereSource()
source.Update()
triangleFilter = vtk.vtkTriangleFilter()
triangleFilter.SetInputConnection(source.GetOutputPort())
triangleFilter.Update()
# Create a mapper and actor
sphereMapper = vtk.vtkDataSetMapper()
sphereMapper.SetInputConnection(triangleFilter.GetOutputPort())
sphereActor = vtk.vtkActor()
sphereActor.SetMapper(sphereMapper)
mesh = triangleFilter.GetOutput()
qualityFilter = vtk.vtkMeshQuality()
qualityFilter.SetInput(mesh)
qualityFilter.SetTriangleQualityMeasureToArea()
qualityFilter.Update()
qualityMesh = qualityFilter.GetOutput()
#qualityArray = vtk.vtkDoubleArray.SafeDownCase(qualityMesh.GetCellData().GetArray("Quality"))
selectCells = vtk.vtkThreshold()
selectCells.ThresholdByLower(0.02)
selectCells.SetInputArrayToProcess(
0, 0, 0, vtk.vtkDataObject.FIELD_ASSOCIATION_CELLS,
vtk.vtkDataSetAttributes.SCALARS)
selectCells.SetInput(qualityMesh)
selectCells.Update()
ug = selectCells.GetOutput()
# Create a mapper and actor
mapper = vtk.vtkDataSetMapper()
mapper.SetInput(ug)
actor = vtk.vtkActor()
actor.SetMapper(mapper)
actor.GetProperty().SetColor(1, 0, 0)
actor.GetProperty().SetRepresentationToWireframe()
actor.GetProperty().SetLineWidth(5)
self.ren.AddActor(sphereActor)
self.ren.AddActor(actor)
self.ren.ResetCamera()
self._initialized = False
def computeTriangleQualityMinAngle(vtkCell):
'''
Returns [ min, average, max, variance, number of cells ] of Minmum included Angleof the polydata's triangles.
Acceptable range = [30°,60°]
for equilateral unit triangle = 60°
reference: Verdict reference manual, Stimpson, 2007
'''
qual = vtk.vtkMeshQuality()
return qual.TriangleMinAngle(vtkCell)
def computeTriangleQualityAspectFrobenius(vtkCell):
'''
Returns [ min, average, max, variance, number of cells ] of Aspect Frobenius of the polydata's triangles.
Aspect Frobenius is defined as q = ( ||L0||^2+||L1||^2+||L2||^2 ) / ( 4*Area*sqrt(3) )
Acceptable range = [1,1.3]
for equilateral unit triangle = 1
reference: Verdict reference manual, Stimpson, 2007
'''
qual = vtk.vtkMeshQuality()
return qual.TriangleAspectFrobenius(vtkCell)
def compute_cells_area(m):
""" numpy array with cells area """
areaf = vtk.vtkMeshQuality()
areaf.SetInputData(m)
areaf.SetTriangleQualityMeasureToArea()
areaf.SaveCellQualityOn() ##default: quality is stored as cell data
areaf.Update()
vtk_x = areaf.GetOutput().GetCellData().GetArray("Quality")
np_x = nps.vtk_to_numpy(vtk_x)
return np_x
def _getElementMetrics(self):
for k, p in self.polydatas.items():
# create a deformed polydata object for deformed metrics
warp = vtk.vtkWarpVector()
warp.SetInputData(p)
warp.SetScaleFactor(1)
p.GetPointData().SetActiveVectors('displacement')
warp.Update()
warped = warp.GetOutput()
# Use the MeshQuality filter with the metric set to volume to quickly get cell volumes
# for reference and deformed cases.
mesh_quality = vtk.vtkMeshQuality()
mesh_quality.SetTetQualityMeasureToVolume()
mesh_quality.SetInputData(p)
mesh_quality.Update()
r_volumes = mesh_quality.GetOutput().GetCellData().GetArray("Quality")
r_volumes.SetName('Reference Volume')
p.GetCellData().AddArray(r_volumes)
mesh_quality2 = vtk.vtkMeshQuality()
mesh_quality2.SetTetQualityMeasureToVolume()
mesh_quality2.SetInputData(warped)
mesh_quality2.Update()
d_volumes = mesh_quality2.GetOutput().GetCellData().GetArray("Quality")
d_volumes.SetName('Deformed Volume')
p.GetCellData().AddArray(d_volumes)
# CellCenters filter generates new polydata with points at centroids. Grab these points
# data array and add it to polydata for reference and deformed.
cell_centers = vtk.vtkCellCenters()
cell_centers.VertexCellsOff()
cell_centers.SetInputData(p)
cell_centers.Update()
r_centroids = cell_centers.GetOutput().GetPoints().GetData()
r_centroids.SetName('Reference Centroid')
p.GetCellData().AddArray(r_centroids)
cell_centers2 = vtk.vtkCellCenters()
cell_centers2.VertexCellsOff()
cell_centers2.SetInputData(warped)
cell_centers2.Update()
d_centroids = cell_centers2.GetOutput().GetPoints().GetData()
d_centroids.SetName('Deformed Centroid')
p.GetCellData().AddArray(d_centroids)
def calculate_area(mesh):
quality = vtk.vtkMeshQuality()
quality.SetInputData(mesh)
quality.SetTriangleQualityMeasureToArea()
quality.Update()
area = quality.GetOutput().GetCellData().GetArray("Quality")
result = np.array(
[area.GetValue(i) for i in range(area.GetNumberOfTuples())])
return result
def computeTriangleQualityRadiusRatio(vtkCell):
'''
Returns [ min, average, max, variance, number of cells ] of Radius Ratio of the polydata's triangles.
Radius ratio is defined as q = ( R ) / ( 2r )
where R = circumradius ( = L0*L1*L2 / ( 2*r*(L0+L1+L2) ) ) and r = inradius ( r = 2*Area/(L0+L1+L2) )
Acceptable range = [1,1.3]
for equilateral unit triangle = 1
reference: Verdict reference manual, Stimpson, 2007
'''
qual = vtk.vtkMeshQuality()
return qual.TriangleRadiusRatio(vtkCell)
def computeTriangleQualityEdgeRatio(vtkCell):
'''
Returns edge ratio of the triangular cell.
Edge Ratio is defined as q = Lmax / Lmin
where Lmax = largest edge Lmin = smallest edge
Acceptable range = [1,1.3]
for equilateral unit triangle = 1
reference: Verdict reference manual, Stimpson, 2007
'''
qual = vtk.vtkMeshQuality()
return qual.TriangleEdgeRatio(vtkCell)
def computeTriangleQualityAspectRatio(vtkCell):
'''
Returns aspect ratio of the triangle.
Aspect Ratio is defined as q = Lmax / ( 2 * sqrt(3) * r ) = Lmax*(L0+L1+L2) / (4*sqrt(3)*Area)
where Lmax = largest edge and r = inradius ( r = 2*Area/(L0+L1+L2) )
Acceptable range = [1,1.3]
for equilateral unit triangle = 1
reference: Verdict reference manual, Stimpson, 2007
'''
qual = vtk.vtkMeshQuality()
return qual.TriangleAspectRatio(vtkCell)
def __init__(self, img, threshold, xysmoothing, zsmoothing, color, alpha):
dataImporter = vtk.vtkImageImport()
simg = np.ascontiguousarray(img, np.uint8)
dataImporter.CopyImportVoidPointer(simg.data, len(simg.data))
dataImporter.SetDataScalarTypeToUnsignedChar()
dataImporter.SetNumberOfScalarComponents(1)
dataImporter.SetDataExtent(0, simg.shape[2]-1, 0, simg.shape[1]-1, 0, simg.shape[0]-1)
dataImporter.SetWholeExtent(0, simg.shape[2]-1, 0, simg.shape[1]-1, 0, simg.shape[0]-1)
self.__smoother = vtk.vtkImageGaussianSmooth()
self.__smoother.SetStandardDeviation(xysmoothing, xysmoothing, zsmoothing)
self.__smoother.SetInputConnection(dataImporter.GetOutputPort())
self.__threshold = vtk.vtkImageThreshold()
self.__threshold.SetInputConnection(self.__smoother.GetOutputPort())
self.__threshold.ThresholdByUpper(threshold)
self.__threshold.ReplaceInOn()
self.__threshold.SetInValue(1)
self.__threshold.ReplaceOutOn()
self.__threshold.SetOutValue(0)
self.__threshold.Update()
contour = vtk.vtkDiscreteMarchingCubes()
contour.SetInputConnection(self.__threshold.GetOutputPort())
contour.ComputeNormalsOn()
contour.SetValue(0, 1)
contour.Update()
smoother = vtk.vtkWindowedSincPolyDataFilter()
smoother.SetInputConnection(contour.GetOutputPort())
smoother.NonManifoldSmoothingOn()
smoother.NormalizeCoordinatesOn()
smoother.Update()
triangleCellNormals=vtk.vtkPolyDataNormals()
triangleCellNormals.SetInputConnection(smoother.GetOutputPort())
triangleCellNormals.ComputeCellNormalsOn()
triangleCellNormals.ComputePointNormalsOff()
triangleCellNormals.ConsistencyOn()
triangleCellNormals.AutoOrientNormalsOn()
triangleCellNormals.Update()
triangleCellAn = vtk.vtkMeshQuality()
triangleCellAn.SetInputConnection(triangleCellNormals.GetOutputPort())
triangleCellAn.SetTriangleQualityMeasureToArea()
triangleCellAn.SaveCellQualityOn()
triangleCellAn.Update()
mapper = vtk.vtkPolyDataMapper()
mapper.SetInputConnection(triangleCellAn.GetOutputPort())
mapper.ScalarVisibilityOn()
mapper.SetScalarRange(.3, 1)
mapper.SetScalarModeToUsePointData()
colorLookupTable = vtk.vtkLookupTable()
colorLookupTable.SetHueRange(.6, 1)
colorLookupTable.Build()
mapper.SetLookupTable(colorLookupTable)
self.SetMapper(mapper)
self.GetProperty().SetColor(*color)
self.GetProperty().SetOpacity(alpha)
def minimal_length(patchData):
""" Compute minimal length as sqrt of smallest area on a patch.
"""
areaFilter = vtk.vtkMeshQuality()
areaFilter.SetInputData(patchData)
areaFilter.SetTriangleQualityMeasureToArea()
areaFilter.SetQuadQualityMeasureToArea()
areaFilter.Update()
area = dsa.WrapDataObject(areaFilter.GetOutput())
area = area.CellData["Quality"]
return np.sqrt(np.min(area))
def test_2D(self):
self.tube.make_2D(self.h / 2)
v1 = self.tube.element_volumes()
writer = writers.VTKWriter(self.tube, "dummy.vtk")
obj = writer.make_vtk_object()
meshQuality = vtk.vtkMeshQuality()
meshQuality.SetInputData(obj)
meshQuality.SetQuadQualityMeasureToArea()
meshQuality.Update()
res = meshQuality.GetOutput()
vols = vtk_to_numpy(res.GetCellData().GetArray("Quality")) * self.h
self.assertTrue(np.allclose(v1, vols, rtol=1e-4))
def test_3D(self):
v1 = self.tube.element_volumes()
writer = writers.VTKWriter(self.tube, "dummy.vtk")
obj = writer.make_vtk_object()
meshQuality = vtk.vtkMeshQuality()
meshQuality.SetInputData(obj)
meshQuality.SetHexQualityMeasureToVolume()
meshQuality.Update()
res = meshQuality.GetOutput()
vols = vtk_to_numpy(res.GetCellData().GetArray("Quality"))
err = np.abs(v1 - vols) / np.abs(vols)
self.assertTrue(np.allclose(v1, vols, rtol=1e-4))
def compute_vtk_volume(data_vtu_in, method="vtk"):
volume = 0
if method == "vtk":
quality = vtk.vtkMeshQuality()
for cell_id in range(data_vtu_in.GetNumberOfCells()):
cell_curr = data_vtu_in.GetCell(cell_id)
vol_curr = quality.TetVolume(cell_curr)
volume = volume + vol_curr
elif method == "abaqus":
if data_vtu_in.GetCellData().HasArray("EVOL"):
cell_volume_array = data_vtu_in.GetCellData().GetArray("EVOL")
for cell_id in range(cell_volume_array.GetNumberOfTuples()):
vol_curr = cell_volume_array.GetValue(cell_id)
volume = volume + vol_curr
print("Volume from '%s': %f" % (method, volume))
return volume
def generateMeshPolyData(points):
pts = v.vtkPoints()
for p in points:
pts.InsertNextPoint(p)
pd = v.vtkPolyData()
pd.SetPoints(pts)
# Create a IdFilter to preserve original point ids
idf = v.vtkIdFilter()
idf.SetIdsArrayName('origIds')
idf.PointIdsOn()
idf.SetInputData(pd)
# Create a 2D Delaunay triangulation
d2d = v.vtkDelaunay2D()
d2d.SetInputConnection(idf.GetOutputPort())
# Create mesh quality cell data array to filter out
# boundary triangles
mq = v.vtkMeshQuality()
mq.SetInputConnection(d2d.GetOutputPort())
mq.SetTriangleQualityMeasureToAspectRatio()
mq.SaveCellQualityOn()
mq.Update()
# Generate the polydata with mesh
plateTriPoly = mq.GetOutput()
plateTri = plateTriPoly.GetPolys()
# Map the connectivity to original point ids
newTriangles = v.vtkCellArray()
plateTri.InitTraversal()
triIds = v.vtkIdList()
origIds = plateTriPoly.GetPointData().GetArray('origIds')
aspectRatioArray = plateTriPoly.GetCellData().GetArray('Quality')
triangleIndex = 0
while plateTri.GetNextCell(triIds):
# Keep only the equilateral triangles to get rid of boundary triangles
aspectRatio = aspectRatioArray.GetTuple1(triangleIndex)
triangleIndex += 1
if aspectRatio < 1.5:
newTriangles.InsertNextCell(3)
for i in range(3):
newTriangles.InsertCellPoint(
int(origIds.GetTuple1(triIds.GetId(i))))
pd.SetPolys(newTriangles)
return pd
def __init__(self, parent = None):
super(VTKFrame, self).__init__(parent)
self.vtkWidget = QVTKRenderWindowInteractor(self)
vl = QtGui.QVBoxLayout(self)
vl.addWidget(self.vtkWidget)
vl.setContentsMargins(0, 0, 0, 0)
self.ren = vtk.vtkRenderer()
self.ren.SetBackground(0.1, 0.2, 0.4)
self.vtkWidget.GetRenderWindow().AddRenderer(self.ren)
self.iren = self.vtkWidget.GetRenderWindow().GetInteractor()
# Create source
source = vtk.vtkSphereSource()
source.Update()
triangleFilter = vtk.vtkTriangleFilter()
triangleFilter.SetInputConnection(source.GetOutputPort())
triangleFilter.Update()
mesh = triangleFilter.GetOutput()
qualityFilter = vtk.vtkMeshQuality()
qualityFilter.SetInput(mesh)
qualityFilter.SetTriangleQualityMeasureToArea()
qualityFilter.Update()
polydata = vtk.vtkPolyData()
polydata.ShallowCopy(qualityFilter.GetOutput())
# Create a mapper and actor
mapper = vtk.vtkDataSetMapper()
mapper.SetInputConnection(polydata.GetProducerPort())
mapper.SetScalarRange(polydata.GetScalarRange())
actor = vtk.vtkActor()
actor.SetMapper(mapper)
self.ren.AddActor(actor)
self.ren.ResetCamera()
self._initialized = False
def computeUgridQualityFrobeniusNorm(ugrid):
'''
reference: Verdict reference manual, Stimpson, 2007
'''
qual = vtk.vtkMeshQuality()
qual.SetInput(ugrid)
qual.VolumeOn()
qual.RatioOn()
qual.SetTetQualityMeasureToFrobeniusNorm()
qual.Update()
return [
qual.GetOutput().GetFieldData().GetArray(
"Mesh Tetrahedron Quality").GetValue(0),
qual.GetOutput().GetFieldData().GetArray(
"Mesh Tetrahedron Quality").GetValue(1),
qual.GetOutput().GetFieldData().GetArray(
"Mesh Tetrahedron Quality").GetValue(2),
qual.GetOutput().GetFieldData().GetArray(
"Mesh Tetrahedron Quality").GetValue(3),
qual.GetOutput().GetFieldData().GetArray(
"Mesh Tetrahedron Quality").GetValue(4)
]
def _clean(self, data):
"""Removes cells that have area less than 1e-10. Also runs the
data through vtkCleanPolyData().
"""
data.BuildLinks()
area = vtk.vtkMeshQuality()
area.SetTriangleQualityMeasureToArea()
area.SetInputData(data)
area.Update()
area = dsa.WrapDataObject(area.GetOutput()).CellData["Quality"]
for i in range(data.GetNumberOfCells()):
if area[i] < 1e-10:
data.DeleteCell(i)
data.RemoveDeletedCells()
cleaner = vtk.vtkCleanPolyData()
cleaner.SetInputData(data)
cleaner.Update()
return cleaner.GetOutput()
def main():
mr = vtk.vtkUnstructuredGridReader()
iq = vtk.vtkMeshQuality()
mr.SetFileName(fname)
mr.Update()
ug = mr.GetOutput()
iq.SetInputConnection(mr.GetOutputPort())
# Here we define the various mesh types and labels for output.
meshTypes = [[
'Triangle', 'Triangle',
[['QualityMeasureToEdgeRatio', ' Edge Ratio:'],
['QualityMeasureToAspectRatio', ' Aspect Ratio:'],
['QualityMeasureToRadiusRatio', ' Radius Ratio:'],
['QualityMeasureToAspectFrobenius', ' Frobenius Norm:'],
['QualityMeasureToMinAngle', ' Minimal Angle:']]
],
[
'Quad', 'Quadrilateral',
[['QualityMeasureToEdgeRatio', ' Edge Ratio:'],
['QualityMeasureToAspectRatio', ' Aspect Ratio:'],
['QualityMeasureToRadiusRatio', ' Radius Ratio:'],
[
'QualityMeasureToMedAspectFrobenius',
' Average Frobenius Norm:'
],
[
'QualityMeasureToMaxAspectFrobenius',
' Maximal Frobenius Norm:'
], ['QualityMeasureToMinAngle', ' Minimal Angle:']]
],
[
'Tet', 'Tetrahedron',
[['QualityMeasureToEdgeRatio', ' Edge Ratio:'],
['QualityMeasureToAspectRatio', ' Aspect Ratio:'],
['QualityMeasureToRadiusRatio', ' Radius Ratio:'],
['QualityMeasureToAspectFrobenius', ' Frobenius Norm:'],
['QualityMeasureToMinAngle', ' Minimal Dihedral Angle:'],
['QualityMeasureToCollapseRatio', ' Collapse Ratio:']]
],
[
'Hex', 'Hexahedron',
[['QualityMeasureToEdgeRatio', ' Edge Ratio:']]
]]
if ug.GetNumberOfCells() > 0:
res = ''
for meshType in meshTypes:
if meshType[0] == 'Tet':
res += '\n%s%s\n %s' % (
'Tetrahedral', ' quality of the mesh:', mr.GetFileName())
elif meshType[0] == 'Hex':
res += '\n%s%s\n %s' % (
'Hexahedral', ' quality of the mesh:', mr.GetFileName())
else:
res += '\n%s%s\n %s' % (meshType[1], ' quality of the mesh:',
mr.GetFileName())
for measure in meshType[2]:
eval('iq.Set' + meshType[0] + measure[0] + '()')
iq.Update()
res += '\n%s\n%s' % (
measure[1],
DumpQualityStats(iq, 'Mesh ' + meshType[1] + ' Quality'))
res += '\n'
print res
#!/usr/bin/env python
import sys
for i in range(0, len(sys.argv)):
if sys.argv[i] == '-A' and i < len(sys.argv)-1:
sys.path = sys.path + [sys.argv[i+1]]
import vtk
from vtk.util.misc import vtkGetDataRoot
filename = vtkGetDataRoot() + '/Data/tetraMesh.vtk'
reader = vtk.vtkUnstructuredGridReader()
reader.SetFileName(filename)
a = vtk.vtkMeshQuality()
a.SetInputConnection(reader.GetOutputPort())
a.VolumeOn()
a.RatioOn()
a.Update()
mesh = a.GetOutput().GetFieldData().GetScalars()
for i in range(mesh.GetNumberOfTuples()):
print mesh.GetTuple2(i)
sys.exit(0)
def Plot_uGridQual(grid):
""" Plots quality of a unstructured grid while ignoring pyramids and wedges """
# Create quality filter
qual_filter = vtk.vtkMeshQuality()
if vtk.vtkVersion().GetVTKMajorVersion() >5:
qual_filter.SetInput(grid)
else:
qual_filter.SetInputData(grid)
qual_filter.SetHexQualityMeasureToScaledJacobian()
qual_filter.SetTetQualityMeasureToScaledJacobian()
qual_filter.SaveCellQualityOn
qual_filter.Update()
qual_out = qual_filter.GetOutput()
# Get quality as array
qual = VN.vtk_to_numpy(qual_out.GetCellData().GetScalars())
# If unstructured then replace quality of pyramids and wedges wtih nans
if str(grid)[:5] =='vtkUnstructuredGrid':
# Get cell types
celltypes = VN.vtk_to_numpy(qual_out.GetCellTypesArray())
# Set quality of wedges and pyramids to 1
wedge_pyr_celltypes = [vtk.vtkWedge().GetCellType(), vtk.vtkPyramid().GetCellType()]
qual[np.in1d(celltypes, wedge_pyr_celltypes)] = 1
# Reinsert quality array back into uGrid
vtkfloat = VN.numpy_to_vtk(np.ascontiguousarray(qual), deep=True)
qual_out.GetCellData().SetScalars(vtkfloat)
# otherwise, negate the grid quality
else:
qual = -qual
vtkfloat = VN.numpy_to_vtk(np.ascontiguousarray(qual), deep=True)
qual_out.GetCellData().SetScalars(vtkfloat)
################################# Plotting #################################
# Create mapper
mapper = vtk.vtkDataSetMapper()
if vtk.vtkVersion().GetVTKMajorVersion() >5:
mapper.SetInput(qual_out)
else:
mapper.SetInputData(qual_out)
mapper.SetScalarRange(np.nanmin(qual), np.nanmax(qual))
# Create Actor
actor = vtk.vtkActor()
actor.SetMapper(mapper)
actor.GetProperty().SetRepresentationToSurface()
actor.GetProperty().EdgeVisibilityOn()
actor.GetProperty().SetColor(1, 1, 1)
actor.GetProperty().LightingOff()
# Add FEM Actor to renderer window
ren = vtk.vtkRenderer()
ren.SetBackground(0.3, 0.3, 0.3)
renWin = vtk.vtkRenderWindow()
renWin.AddRenderer(ren)
iren = vtk.vtkRenderWindowInteractor()
iren.SetRenderWindow(renWin)
# Allow user to interact
istyle = vtk.vtkInteractorStyleTrackballCamera()
iren.SetInteractorStyle(istyle)
# Add surface to display
ren.AddActor(actor)
# Add scalar bar
scalarBar = vtk.vtkScalarBarActor()
scalarBar.SetLookupTable(mapper.GetLookupTable())
scalarBar.SetTitle('Quality')
scalarBar.SetNumberOfLabels(5)
ren.AddActor(scalarBar)
# Render
iren.Initialize()
renWin.Render()
renWin.SetWindowName('FEM Element Quality')
iren.Start()
def main():
mr = vtk.vtkUnstructuredGridReader()
iq = vtk.vtkMeshQuality()
mr.SetFileName(fname)
mr.Update()
ug = mr.GetOutput()
iq.SetInputConnection(mr.GetOutputPort())
# Here we define the various mesh types and labels for output.
meshTypes = [['Triangle', 'Triangle',
[['QualityMeasureToEdgeRatio', ' Edge Ratio:'],
['QualityMeasureToAspectRatio', ' Aspect Ratio:'],
['QualityMeasureToRadiusRatio', ' Radius Ratio:'],
['QualityMeasureToAspectFrobenius', ' Frobenius Norm:'],
['QualityMeasureToMinAngle', ' Minimal Angle:']
]
],
['Quad', 'Quadrilateral',
[['QualityMeasureToEdgeRatio', ' Edge Ratio:'],
['QualityMeasureToAspectRatio', ' Aspect Ratio:'],
['QualityMeasureToRadiusRatio', ' Radius Ratio:'],
['QualityMeasureToMedAspectFrobenius',
' Average Frobenius Norm:'],
['QualityMeasureToMaxAspectFrobenius',
' Maximal Frobenius Norm:'],
['QualityMeasureToMinAngle', ' Minimal Angle:']
]
],
['Tet', 'Tetrahedron',
[['QualityMeasureToEdgeRatio', ' Edge Ratio:'],
['QualityMeasureToAspectRatio', ' Aspect Ratio:'],
['QualityMeasureToRadiusRatio', ' Radius Ratio:'],
['QualityMeasureToAspectFrobenius', ' Frobenius Norm:'],
['QualityMeasureToMinAngle', ' Minimal Dihedral Angle:'],
['QualityMeasureToCollapseRatio', ' Collapse Ratio:']
]
],
['Hex', 'Hexahedron',
[['QualityMeasureToEdgeRatio', ' Edge Ratio:']
]
]
]
if ug.GetNumberOfCells() > 0 :
res = ''
for meshType in meshTypes:
if meshType[0] == 'Tet':
res += '\n%s%s\n %s' % ('Tetrahedral',
' quality of the mesh:', mr.GetFileName())
elif meshType[0] == 'Hex':
res += '\n%s%s\n %s' % ('Hexahedral',
' quality of the mesh:', mr.GetFileName())
else:
res += '\n%s%s\n %s' % (meshType[1],
' quality of the mesh:', mr.GetFileName())
for measure in meshType[2]:
eval('iq.Set' + meshType[0] + measure[0] + '()')
iq.Update()
res += '\n%s\n%s' % (measure[1],
DumpQualityStats(iq, 'Mesh ' + meshType[1] + ' Quality'))
res += '\n'
print res
def read_data_and_differentiate(pod_mode_dir,num_modes,num_points,num_boundary_faces,num_dimensions,num_components,correct_for_cell_volumes, \
u,v,w,dudx,dudy,dudz,dvdx,dvdy,dvdz,dwdx,dwdy,dwdz,\
uF,vF,wF,dudxF,dudyF,dudzF,dvdxF,dvdyF,dvdzF,dwdxF,dwdyF,dwdzF,cell_volume,norm,calibrate_coefficients):
u_read = np.array(np.zeros((num_points,3), dtype=np.float64))
dudx_read = np.array(np.zeros((num_points,3,3), dtype=np.float64))
uF_read = np.array(np.zeros((num_boundary_faces,3), dtype=np.float64))
dudxF_read = np.array(np.zeros((num_boundary_faces,3,3), dtype=np.float64))
# ..................................................
# Read meanfield and spatially differentiate
filename = pod_mode_dir + "/spatial_meanfield.vtk"
print ' Reading file ', filename.strip()
reader = vtk.vtkUnstructuredGridReader()
reader.ReadAllScalarsOn()
reader.ReadAllVectorsOn()
reader.ReadAllTensorsOn()
reader.SetFileName(filename)
reader.Update()
grid = vtk.vtkUnstructuredGrid()
grid.DeepCopy(reader.GetOutput())
# get cell volumes
if (correct_for_cell_volumes=="true"):
cell_volume[:] = VN.vtk_to_numpy(grid.GetPointData().GetScalars("cell_volume"))
else:
cell_volume[:] = 1.0
# get mean velocity field within volume
u_read = VN.vtk_to_numpy(grid.GetPointData().GetVectors("u"))
u[:,0] = u_read[:,0].copy()
v[:,0] = u_read[:,1].copy()
w[:,0] = u_read[:,2].copy()
grid.GetPointData().SetVectors(grid.GetPointData().GetVectors("u"))
# get mean velocity derivative field within volume
differentiator = vtk.vtkCellDerivatives()
differentiator.SetTensorModeToComputeGradient()
differentiator.SetInput(grid)
differentiator.Update()
cell_to_point_data = vtk.vtkCellDataToPointData()
cell_to_point_data.SetInput(differentiator.GetOutput())
cell_to_point_data.Update()
grid.GetPointData().SetTensors(cell_to_point_data.GetOutput().GetPointData().GetTensors())
dudx_read = VN.vtk_to_numpy(cell_to_point_data.GetOutput().GetPointData().GetTensors())
dudx[:,0] = dudx_read[:,0].copy()
dvdx[:,0] = dudx_read[:,1].copy()
dwdx[:,0] = dudx_read[:,2].copy()
dudy[:,0] = dudx_read[:,3].copy()
dvdy[:,0] = dudx_read[:,4].copy()
dwdy[:,0] = dudx_read[:,5].copy()
dudz[:,0] = dudx_read[:,6].copy()
dvdz[:,0] = dudx_read[:,7].copy()
dwdz[:,0] = dudx_read[:,8].copy()
# extract boundary surface data
if( (calibrate_coefficients=="none") or (calibrate_coefficients=="constant") ):
geom_filter = vtk.vtkDataSetSurfaceFilter()
geom_filter.SetInput(grid)
geom_filter.Update()
boundary_faces = vtk.vtkPolyData()
boundary_faces = geom_filter.GetOutput()
point_to_cell_data = vtk.vtkPointDataToCellData()
point_to_cell_data.SetInput(geom_filter.GetOutput())
point_to_cell_data.Update()
# get mean velocity field on boundary surface
uF_read = VN.vtk_to_numpy(point_to_cell_data.GetOutput().GetCellData().GetVectors("u"))
uF[:,0] = uF_read[:,0]
vF[:,0] = uF_read[:,1]
wF[:,0] = uF_read[:,2]
# get mean derivative velocity field on boundary surface
dudxF_read = VN.vtk_to_numpy(point_to_cell_data.GetOutput().GetCellData().GetTensors())
dudxF[:,0] = dudxF_read[:,0]
dvdxF[:,0] = dudxF_read[:,1]
dwdxF[:,0] = dudxF_read[:,2]
dudyF[:,0] = dudxF_read[:,3]
dvdyF[:,0] = dudxF_read[:,4]
dwdyF[:,0] = dudxF_read[:,5]
dudzF[:,0] = dudxF_read[:,6]
dvdzF[:,0] = dudxF_read[:,7]
dwdzF[:,0] = dudxF_read[:,8]
# get boundary face normals
norm_filter = vtk.vtkPolyDataNormals()
norm_filter.ComputeCellNormalsOn()
norm_filter.SetInput(boundary_faces)
norm_filter.Update()
area_filter = vtk.vtkMeshQuality()
area_filter.SetQuadQualityMeasureToArea()
area_filter.SetTriangleQualityMeasureToArea()
area_filter.SetInput(boundary_faces)
area_filter.Update()
for j in range(0,num_boundary_faces):
area = area_filter.GetOutput().GetCellData().GetArray("Quality").GetComponent(j,0)
norm[j,:] = norm_filter.GetOutput().GetCellData().GetNormals().GetTuple(j)
norm[j,:] = norm[j,:] * area
# ..................................................
# Read modes and spatially differentiate
for j in range(0,num_modes):
j_index = j+1
filename = pod_mode_dir + '/POD.spatial_mode_' + '%04d'%j_index + '.vtk'
print ' Reading file ', filename.strip(), 'file number ', j_index, ' of ', num_modes
reader.SetFileName(filename)
reader.Update()
# get mode velocity field within volume
u_read = VN.vtk_to_numpy(reader.GetOutput().GetPointData().GetVectors("u"))
u[:,j_index] = u_read[:,0]
v[:,j_index] = u_read[:,1]
w[:,j_index] = u_read[:,2]
# get mode velocity derivative fields within volume
grid.GetPointData().SetVectors(reader.GetOutput().GetPointData().GetVectors("u"))
differentiator.SetInput(grid)
differentiator.Update()
cell_to_point_data.SetInput(differentiator.GetOutput())
cell_to_point_data.Update()
grid.GetPointData().SetTensors(cell_to_point_data.GetOutput().GetPointData().GetTensors())
dudx_read = VN.vtk_to_numpy(cell_to_point_data.GetOutput().GetPointData().GetTensors())
dudx[:,j_index] = dudx_read[:,0]
dvdx[:,j_index] = dudx_read[:,1]
dwdx[:,j_index] = dudx_read[:,2]
dudy[:,j_index] = dudx_read[:,3]
dvdy[:,j_index] = dudx_read[:,4]
dwdy[:,j_index] = dudx_read[:,5]
dudz[:,j_index] = dudx_read[:,6]
dvdz[:,j_index] = dudx_read[:,7]
dwdz[:,j_index] = dudx_read[:,8]
# extract boundary surface data
if( (calibrate_coefficients=="none") or (calibrate_coefficients=="constant") ):
geom_filter.SetInput(grid)
geom_filter.Update()
boundary_faces = geom_filter.GetOutput()
point_to_cell_data.SetInput(geom_filter.GetOutput())
point_to_cell_data.Update()
# get mode velocity field on boundary surface
uF_read = VN.vtk_to_numpy(point_to_cell_data.GetOutput().GetCellData().GetVectors("u"))
uF[:,j_index] = uF_read[:,0]
vF[:,j_index] = uF_read[:,1]
wF[:,j_index] = uF_read[:,2]
# get mean derivative velocity field on boundary surface
dudxF_read = VN.vtk_to_numpy(point_to_cell_data.GetOutput().GetCellData().GetTensors())
dudxF[:,j_index] = dudxF_read[:,0]
dvdxF[:,j_index] = dudxF_read[:,1]
dwdxF[:,j_index] = dudxF_read[:,2]
dudyF[:,j_index] = dudxF_read[:,3]
dvdyF[:,j_index] = dudxF_read[:,4]
dwdyF[:,j_index] = dudxF_read[:,5]
dudzF[:,j_index] = dudxF_read[:,6]
dvdzF[:,j_index] = dudxF_read[:,7]
dwdzF[:,j_index] = dudxF_read[:,8]
# ..................................................
# zero appropriate coefficients
if (num_dimensions<3):
dudz[:,:] = 0.0
dvdz[:,:] = 0.0
dwdz[:,:] = 0.0
if (num_dimensions<2):
dudy[:,:] = 0.0
dvdy[:,:] = 0.0
dwdy[:,:] = 0.0
if (num_components<3):
w[:,:] = 0.0
dwdx[:,:] = 0.0
dwdy[:,:] = 0.0
dwdz[:,:] = 0.0
if (num_components<2):
v[:,:] = 0.0
dvdx[:,:] = 0.0
dvdy[:,:] = 0.0
dvdz[:,:] = 0.0
if( (calibrate_coefficients=="none") or (calibrate_coefficients=="constant") ):
if (num_dimensions<3):
dudzF[:,:] = 0.0
dvdzF[:,:] = 0.0
dwdzF[:,:] = 0.0
if (num_dimensions<2):
dudyF[:,:] = 0.0
dvdyF[:,:] = 0.0
dwdyF[:,:] = 0.0
if (num_components<3):
wF[:,j_index] = 0.0
dwdxF[:,:] = 0.0
dwdyF[:,:] = 0.0
dwdzF[:,:] = 0.0
if (num_components<2):
vF[:,:] = 0.0
dvdxF[:,:] = 0.0
dvdyF[:,:] = 0.0
dvdzF[:,:] = 0.0
def read_data_and_differentiate(pod_mode_dir,num_modes,num_points,num_boundary_faces,num_dimensions,num_components,correct_for_cell_volumes, \
u,v,w,dudx,dudy,dudz,dvdx,dvdy,dvdz,dwdx,dwdy,dwdz,\
uF,vF,wF,dudxF,dudyF,dudzF,dvdxF,dvdyF,dvdzF,dwdxF,dwdyF,dwdzF,cell_volume,norm,calibrate_coefficients):
u_read = np.array(np.zeros((num_points, 3), dtype=np.float64))
dudx_read = np.array(np.zeros((num_points, 3, 3), dtype=np.float64))
uF_read = np.array(np.zeros((num_boundary_faces, 3), dtype=np.float64))
dudxF_read = np.array(
np.zeros((num_boundary_faces, 3, 3), dtype=np.float64))
# ..................................................
# Read meanfield and spatially differentiate
filename = pod_mode_dir + "/spatial_meanfield.vtk"
print ' Reading file ', filename.strip()
reader = vtk.vtkUnstructuredGridReader()
reader.ReadAllScalarsOn()
reader.ReadAllVectorsOn()
reader.ReadAllTensorsOn()
reader.SetFileName(filename)
reader.Update()
grid = vtk.vtkUnstructuredGrid()
grid.DeepCopy(reader.GetOutput())
# get cell volumes
if (correct_for_cell_volumes == "true"):
cell_volume[:] = VN.vtk_to_numpy(
grid.GetPointData().GetScalars("cell_volume"))
else:
cell_volume[:] = 1.0
# get mean velocity field within volume
u_read = VN.vtk_to_numpy(grid.GetPointData().GetVectors("u"))
u[:, 0] = u_read[:, 0].copy()
v[:, 0] = u_read[:, 1].copy()
w[:, 0] = u_read[:, 2].copy()
grid.GetPointData().SetVectors(grid.GetPointData().GetVectors("u"))
# get mean velocity derivative field within volume
differentiator = vtk.vtkCellDerivatives()
differentiator.SetTensorModeToComputeGradient()
differentiator.SetInput(grid)
differentiator.Update()
cell_to_point_data = vtk.vtkCellDataToPointData()
cell_to_point_data.SetInput(differentiator.GetOutput())
cell_to_point_data.Update()
grid.GetPointData().SetTensors(
cell_to_point_data.GetOutput().GetPointData().GetTensors())
dudx_read = VN.vtk_to_numpy(
cell_to_point_data.GetOutput().GetPointData().GetTensors())
dudx[:, 0] = dudx_read[:, 0].copy()
dvdx[:, 0] = dudx_read[:, 1].copy()
dwdx[:, 0] = dudx_read[:, 2].copy()
dudy[:, 0] = dudx_read[:, 3].copy()
dvdy[:, 0] = dudx_read[:, 4].copy()
dwdy[:, 0] = dudx_read[:, 5].copy()
dudz[:, 0] = dudx_read[:, 6].copy()
dvdz[:, 0] = dudx_read[:, 7].copy()
dwdz[:, 0] = dudx_read[:, 8].copy()
# extract boundary surface data
if ((calibrate_coefficients == "none")
or (calibrate_coefficients == "constant")):
geom_filter = vtk.vtkDataSetSurfaceFilter()
geom_filter.SetInput(grid)
geom_filter.Update()
boundary_faces = vtk.vtkPolyData()
boundary_faces = geom_filter.GetOutput()
point_to_cell_data = vtk.vtkPointDataToCellData()
point_to_cell_data.SetInput(geom_filter.GetOutput())
point_to_cell_data.Update()
# get mean velocity field on boundary surface
uF_read = VN.vtk_to_numpy(
point_to_cell_data.GetOutput().GetCellData().GetVectors("u"))
uF[:, 0] = uF_read[:, 0]
vF[:, 0] = uF_read[:, 1]
wF[:, 0] = uF_read[:, 2]
# get mean derivative velocity field on boundary surface
dudxF_read = VN.vtk_to_numpy(
point_to_cell_data.GetOutput().GetCellData().GetTensors())
dudxF[:, 0] = dudxF_read[:, 0]
dvdxF[:, 0] = dudxF_read[:, 1]
dwdxF[:, 0] = dudxF_read[:, 2]
dudyF[:, 0] = dudxF_read[:, 3]
dvdyF[:, 0] = dudxF_read[:, 4]
dwdyF[:, 0] = dudxF_read[:, 5]
dudzF[:, 0] = dudxF_read[:, 6]
dvdzF[:, 0] = dudxF_read[:, 7]
dwdzF[:, 0] = dudxF_read[:, 8]
# get boundary face normals
norm_filter = vtk.vtkPolyDataNormals()
norm_filter.ComputeCellNormalsOn()
norm_filter.SetInput(boundary_faces)
norm_filter.Update()
area_filter = vtk.vtkMeshQuality()
area_filter.SetQuadQualityMeasureToArea()
area_filter.SetTriangleQualityMeasureToArea()
area_filter.SetInput(boundary_faces)
area_filter.Update()
for j in range(0, num_boundary_faces):
area = area_filter.GetOutput().GetCellData().GetArray(
"Quality").GetComponent(j, 0)
norm[j, :] = norm_filter.GetOutput().GetCellData().GetNormals(
).GetTuple(j)
norm[j, :] = norm[j, :] * area
# ..................................................
# Read modes and spatially differentiate
for j in range(0, num_modes):
j_index = j + 1
filename = pod_mode_dir + '/POD.spatial_mode_' + '%04d' % j_index + '.vtk'
print ' Reading file ', filename.strip(
), 'file number ', j_index, ' of ', num_modes
reader.SetFileName(filename)
reader.Update()
# get mode velocity field within volume
u_read = VN.vtk_to_numpy(
reader.GetOutput().GetPointData().GetVectors("u"))
u[:, j_index] = u_read[:, 0]
v[:, j_index] = u_read[:, 1]
w[:, j_index] = u_read[:, 2]
# get mode velocity derivative fields within volume
grid.GetPointData().SetVectors(
reader.GetOutput().GetPointData().GetVectors("u"))
differentiator.SetInput(grid)
differentiator.Update()
cell_to_point_data.SetInput(differentiator.GetOutput())
cell_to_point_data.Update()
grid.GetPointData().SetTensors(
cell_to_point_data.GetOutput().GetPointData().GetTensors())
dudx_read = VN.vtk_to_numpy(
cell_to_point_data.GetOutput().GetPointData().GetTensors())
dudx[:, j_index] = dudx_read[:, 0]
dvdx[:, j_index] = dudx_read[:, 1]
dwdx[:, j_index] = dudx_read[:, 2]
dudy[:, j_index] = dudx_read[:, 3]
dvdy[:, j_index] = dudx_read[:, 4]
dwdy[:, j_index] = dudx_read[:, 5]
dudz[:, j_index] = dudx_read[:, 6]
dvdz[:, j_index] = dudx_read[:, 7]
dwdz[:, j_index] = dudx_read[:, 8]
# extract boundary surface data
if ((calibrate_coefficients == "none")
or (calibrate_coefficients == "constant")):
geom_filter.SetInput(grid)
geom_filter.Update()
boundary_faces = geom_filter.GetOutput()
point_to_cell_data.SetInput(geom_filter.GetOutput())
point_to_cell_data.Update()
# get mode velocity field on boundary surface
uF_read = VN.vtk_to_numpy(
point_to_cell_data.GetOutput().GetCellData().GetVectors("u"))
uF[:, j_index] = uF_read[:, 0]
vF[:, j_index] = uF_read[:, 1]
wF[:, j_index] = uF_read[:, 2]
# get mean derivative velocity field on boundary surface
dudxF_read = VN.vtk_to_numpy(
point_to_cell_data.GetOutput().GetCellData().GetTensors())
dudxF[:, j_index] = dudxF_read[:, 0]
dvdxF[:, j_index] = dudxF_read[:, 1]
dwdxF[:, j_index] = dudxF_read[:, 2]
dudyF[:, j_index] = dudxF_read[:, 3]
dvdyF[:, j_index] = dudxF_read[:, 4]
dwdyF[:, j_index] = dudxF_read[:, 5]
dudzF[:, j_index] = dudxF_read[:, 6]
dvdzF[:, j_index] = dudxF_read[:, 7]
dwdzF[:, j_index] = dudxF_read[:, 8]
# ..................................................
# zero appropriate coefficients
if (num_dimensions < 3):
dudz[:, :] = 0.0
dvdz[:, :] = 0.0
dwdz[:, :] = 0.0
if (num_dimensions < 2):
dudy[:, :] = 0.0
dvdy[:, :] = 0.0
dwdy[:, :] = 0.0
if (num_components < 3):
w[:, :] = 0.0
dwdx[:, :] = 0.0
dwdy[:, :] = 0.0
dwdz[:, :] = 0.0
if (num_components < 2):
v[:, :] = 0.0
dvdx[:, :] = 0.0
dvdy[:, :] = 0.0
dvdz[:, :] = 0.0
if ((calibrate_coefficients == "none")
or (calibrate_coefficients == "constant")):
if (num_dimensions < 3):
dudzF[:, :] = 0.0
dvdzF[:, :] = 0.0
dwdzF[:, :] = 0.0
if (num_dimensions < 2):
dudyF[:, :] = 0.0
dvdyF[:, :] = 0.0
dwdyF[:, :] = 0.0
if (num_components < 3):
wF[:, j_index] = 0.0
dwdxF[:, :] = 0.0
dwdyF[:, :] = 0.0
dwdzF[:, :] = 0.0
if (num_components < 2):
vF[:, :] = 0.0
dvdxF[:, :] = 0.0
dvdyF[:, :] = 0.0
dvdzF[:, :] = 0.0
def _getECMstrain(self):
"""
Generates tetrahedrons from object centroids in the reference and deformed states.
The highest quality tetrahedron (edge ratio closest to 1) is used to construct a
linear system of equations,
:math:`\|\mathbf{w}\|^2 - \|\mathbf{W}\|^2 = \mathbf{W}.\mathbf{E}.\mathbf{W}`,
where, :math:`\mathbf{W}` are the reference tetrahedron edges (as vectors) and
:math:`\mathbf{w}` are the deformed tetrahedron edges, to solve for Green-Lagrange
strain, :math:`\mathbf{E}`.
Returns
-------
ecm_strain
"""
#get the ECM strain
rc = np.array(self.rcentroids)
dc = np.array(self.dcentroids)
if rc.shape[0] < 4:
print(("WARNING: There are less than 4 objects in the space; "
"therefore, tissue strain was not calculated."))
return
da = numpy_to_vtk(rc)
p = vtk.vtkPoints()
p.SetData(da)
pd = vtk.vtkPolyData()
pd.SetPoints(p)
tet = vtk.vtkDelaunay3D()
tet.SetInputData(pd)
tet.Update()
quality = vtk.vtkMeshQuality()
quality.SetInputData(tet.GetOutput())
quality.Update()
mq = quality.GetOutput().GetCellData().GetArray("Quality")
mq = vtk_to_numpy(mq)
try:
#tet with edge ratio closest to 1
btet = np.argmin(abs(mq - 1.0))
except:
return
idlist = tet.GetOutput().GetCell(btet).GetPointIds()
P = np.zeros((4, 3), float)
p = np.zeros((4, 3), float)
for i in range(idlist.GetNumberOfIds()):
P[i, :] = rc[idlist.GetId(i), :]
p[i, :] = dc[idlist.GetId(i), :]
X = np.array([P[1, :] - P[0, :],
P[2, :] - P[0, :],
P[3, :] - P[0, :],
P[3, :] - P[1, :],
P[3, :] - P[2, :],
P[2, :] - P[1, :]], float)
x = np.array([p[1, :] - p[0, :],
p[2, :] - p[0, :],
p[3, :] - p[0, :],
p[3, :] - p[1, :],
p[3, :] - p[2, :],
p[2, :] - p[1, :]], float)
#assemble the system
dX = np.zeros((6, 6), float)
ds = np.zeros((6, 1), float)
for i in range(6):
dX[i, 0] = 2 * X[i, 0] ** 2
dX[i, 1] = 2 * X[i, 1] ** 2
dX[i, 2] = 2 * X[i, 2] ** 2
dX[i, 3] = 4 * X[i, 0] * X[i, 1]
dX[i, 4] = 4 * X[i, 0] * X[i, 2]
dX[i, 5] = 4 * X[i, 1] * X[i, 2]
ds[i, 0] = np.linalg.norm(
x[i, :]) ** 2 - np.linalg.norm(X[i, :]) ** 2
E = np.linalg.solve(dX, ds)
E = np.array([[E[0, 0], E[3, 0], E[4, 0]],
[E[3, 0], E[1, 0], E[5, 0]],
[E[4, 0], E[5, 0], E[2, 0]]], float)
self.ecm_strain = E
def Plot_uGridQual(grid):
""" Plots quality of a unstructured grid while ignoring pyramids and wedges """
# Create quality filter
qual_filter = vtk.vtkMeshQuality()
if vtk.vtkVersion().GetVTKMajorVersion() > 5:
qual_filter.SetInput(grid)
else:
qual_filter.SetInputData(grid)
qual_filter.SetHexQualityMeasureToScaledJacobian()
qual_filter.SetTetQualityMeasureToScaledJacobian()
qual_filter.SaveCellQualityOn
qual_filter.Update()
qual_out = qual_filter.GetOutput()
# Get quality as array
qual = VN.vtk_to_numpy(qual_out.GetCellData().GetScalars())
# If unstructured then replace quality of pyramids and wedges wtih nans
if str(grid)[:5] == 'vtkUnstructuredGrid':
# Get cell types
celltypes = VN.vtk_to_numpy(qual_out.GetCellTypesArray())
# Set quality of wedges and pyramids to 1
wedge_pyr_celltypes = [
vtk.vtkWedge().GetCellType(),
vtk.vtkPyramid().GetCellType()
]
qual[np.in1d(celltypes, wedge_pyr_celltypes)] = 1
# Reinsert quality array back into uGrid
vtkfloat = VN.numpy_to_vtk(np.ascontiguousarray(qual), deep=True)
qual_out.GetCellData().SetScalars(vtkfloat)
# otherwise, negate the grid quality
else:
qual = -qual
vtkfloat = VN.numpy_to_vtk(np.ascontiguousarray(qual), deep=True)
qual_out.GetCellData().SetScalars(vtkfloat)
################################# Plotting #################################
# Create mapper
mapper = vtk.vtkDataSetMapper()
if vtk.vtkVersion().GetVTKMajorVersion() > 5:
mapper.SetInput(qual_out)
else:
mapper.SetInputData(qual_out)
mapper.SetScalarRange(np.nanmin(qual), np.nanmax(qual))
# Create Actor
actor = vtk.vtkActor()
actor.SetMapper(mapper)
actor.GetProperty().SetRepresentationToSurface()
actor.GetProperty().EdgeVisibilityOn()
actor.GetProperty().SetColor(1, 1, 1)
actor.GetProperty().LightingOff()
# Add FEM Actor to renderer window
ren = vtk.vtkRenderer()
ren.SetBackground(0.3, 0.3, 0.3)
renWin = vtk.vtkRenderWindow()
renWin.AddRenderer(ren)
iren = vtk.vtkRenderWindowInteractor()
iren.SetRenderWindow(renWin)
# Allow user to interact
istyle = vtk.vtkInteractorStyleTrackballCamera()
iren.SetInteractorStyle(istyle)
# Add surface to display
ren.AddActor(actor)
# Add scalar bar
scalarBar = vtk.vtkScalarBarActor()
scalarBar.SetLookupTable(mapper.GetLookupTable())
scalarBar.SetTitle('Quality')
scalarBar.SetNumberOfLabels(5)
ren.AddActor(scalarBar)
# Render
iren.Initialize()
renWin.Render()
renWin.SetWindowName('FEM Element Quality')
iren.Start()
smoother.Update()
##calc cell normal
triangleCellNormals = vtk.vtkPolyDataNormals()
if vtk.VTK_MAJOR_VERSION <= 5:
triangleCellNormals.SetInput(smoother.GetOutput())
else:
triangleCellNormals.SetInputConnection(smoother.GetOutputPort())
triangleCellNormals.ComputeCellNormalsOn()
triangleCellNormals.ComputePointNormalsOff()
triangleCellNormals.ConsistencyOn()
triangleCellNormals.AutoOrientNormalsOn()
triangleCellNormals.Update() #creates vtkPolyData
##calc cell area
triangleCellAN = vtk.vtkMeshQuality()
if vtk.VTK_MAJOR_VERSION <= 5:
triangleCellAN.SetInput(triangleCellNormals.GetOutput())
else:
triangleCellAN.SetInputConnection(triangleCellNormals.GetOutputPort())
triangleCellAN.SetTriangleQualityMeasureToArea()
triangleCellAN.SaveCellQualityOn() #default
triangleCellAN.Update() #creates vtkDataSet
PointNormalArray = triangleCellNormals.GetOutput().GetCellData(
).GetNormals()
qualityArray = triangleCellAN.GetOutput().GetCellData().GetArray("Quality")
if (PointNormalArray.GetNumberOfTuples() !=
qualityArray.GetNumberOfTuples()):
print "Error! Sizes of normal array and area array dont equal!"
##calc cell normal
triangle_cell_normals = vtk.vtkPolyDataNormals()
if vtk.VTK_MAJOR_VERSION <= 5:
triangle_cell_normals.SetInput(smoother.GetOutput())
else:
triangle_cell_normals.SetInputConnection(smoother.GetOutputPort())
triangle_cell_normals.ComputeCellNormalsOn()
triangle_cell_normals.ComputePointNormalsOff()
triangle_cell_normals.ConsistencyOn()
triangle_cell_normals.AutoOrientNormalsOn()
triangle_cell_normals.Update() #creates vtkPolyData
##calc cell area
triangle_cell_mesh_quality = vtk.vtkMeshQuality()
if vtk.VTK_MAJOR_VERSION <= 5:
triangle_cell_mesh_quality.SetInput(triangle_cell_normals.GetOutput())
else:
triangle_cell_mesh_quality.SetInputConnection(triangle_cell_normals.GetOutputPort())
triangle_cell_mesh_quality.SetTriangleQualityMeasureToArea()
triangle_cell_mesh_quality.SaveCellQualityOn() #default
triangle_cell_mesh_quality.Update() #creates vtkDataSet
point_normal_array = triangle_cell_normals.GetOutput().GetCellData().GetNormals()
quality_array = triangle_cell_mesh_quality.GetOutput().GetCellData().GetArray("Quality")
if point_normal_array.GetNumberOfTuples() != qualityArray.GetNumberOfTuples():
print "Error! Sizes of normal array and area array dont equal!"
exit(1)
def _getECMstrain(self):
"""
Generates tetrahedrons from object centroids in the reference and deformed states.
The highest quality tetrahedron (edge ratio closest to 1) is used to construct a
linear system of equations,
:math:`\|\mathbf{w}\|^2 - \|\mathbf{W}\|^2 = \mathbf{W}.\mathbf{E}.\mathbf{W}`,
where, :math:`\mathbf{W}` are the reference tetrahedron edges (as vectors) and
:math:`\mathbf{w}` are the deformed tetrahedron edges, to solve for Green-Lagrange
strain, :math:`\mathbf{E}`.
Returns
-------
ecm_strain
"""
#get the ECM strain
rc = np.array(self.rcentroids)
dc = np.array(self.dcentroids)
if rc.shape[0] < 4:
print(("WARNING: There are less than 4 objects in the space; "
"therefore, tissue strain was not calculated."))
return
da = numpy_to_vtk(rc)
p = vtk.vtkPoints()
p.SetData(da)
pd = vtk.vtkPolyData()
pd.SetPoints(p)
tet = vtk.vtkDelaunay3D()
tet.SetInputData(pd)
tet.Update()
quality = vtk.vtkMeshQuality()
quality.SetInputData(tet.GetOutput())
quality.Update()
mq = quality.GetOutput().GetCellData().GetArray("Quality")
mq = vtk_to_numpy(mq)
try:
#tet with edge ratio closest to 1
btet = np.argmin(abs(mq - 1.0))
except:
return
idlist = tet.GetOutput().GetCell(btet).GetPointIds()
P = np.zeros((4, 3), float)
p = np.zeros((4, 3), float)
for i in range(idlist.GetNumberOfIds()):
P[i, :] = rc[idlist.GetId(i), :]
p[i, :] = dc[idlist.GetId(i), :]
X = np.array([
P[1, :] - P[0, :], P[2, :] - P[0, :], P[3, :] - P[0, :],
P[3, :] - P[1, :], P[3, :] - P[2, :], P[2, :] - P[1, :]
], float)
x = np.array([
p[1, :] - p[0, :], p[2, :] - p[0, :], p[3, :] - p[0, :],
p[3, :] - p[1, :], p[3, :] - p[2, :], p[2, :] - p[1, :]
], float)
#assemble the system
dX = np.zeros((6, 6), float)
ds = np.zeros((6, 1), float)
for i in range(6):
dX[i, 0] = 2 * X[i, 0]**2
dX[i, 1] = 2 * X[i, 1]**2
dX[i, 2] = 2 * X[i, 2]**2
dX[i, 3] = 4 * X[i, 0] * X[i, 1]
dX[i, 4] = 4 * X[i, 0] * X[i, 2]
dX[i, 5] = 4 * X[i, 1] * X[i, 2]
ds[i, 0] = np.linalg.norm(x[i, :])**2 - np.linalg.norm(X[i, :])**2
E = np.linalg.solve(dX, ds)
E = np.array([[E[0, 0], E[3, 0], E[4, 0]], [E[3, 0], E[1, 0], E[5, 0]],
[E[4, 0], E[5, 0], E[2, 0]]], float)
self.ecm_strain = E
def main():
mr = vtk.vtkUnstructuredGridReader()
iq = vtk.vtkMeshQuality()
mr.SetFileName(fname)
mr.Update()
ug = mr.GetOutput()
iq.SetInputConnection(mr.GetOutputPort())
# Here we define the various mesh types and labels for output.
meshTypes = [
[
"Triangle",
"Triangle",
[
["QualityMeasureToEdgeRatio", " Edge Ratio:"],
["QualityMeasureToAspectRatio", " Aspect Ratio:"],
["QualityMeasureToRadiusRatio", " Radius Ratio:"],
["QualityMeasureToAspectFrobenius", " Frobenius Norm:"],
["QualityMeasureToMinAngle", " Minimal Angle:"],
],
],
[
"Quad",
"Quadrilateral",
[
["QualityMeasureToEdgeRatio", " Edge Ratio:"],
["QualityMeasureToAspectRatio", " Aspect Ratio:"],
["QualityMeasureToRadiusRatio", " Radius Ratio:"],
["QualityMeasureToMedAspectFrobenius", " Average Frobenius Norm:"],
["QualityMeasureToMaxAspectFrobenius", " Maximal Frobenius Norm:"],
["QualityMeasureToMinAngle", " Minimal Angle:"],
],
],
[
"Tet",
"Tetrahedron",
[
["QualityMeasureToEdgeRatio", " Edge Ratio:"],
["QualityMeasureToAspectRatio", " Aspect Ratio:"],
["QualityMeasureToRadiusRatio", " Radius Ratio:"],
["QualityMeasureToAspectFrobenius", " Frobenius Norm:"],
["QualityMeasureToMinAngle", " Minimal Dihedral Angle:"],
["QualityMeasureToCollapseRatio", " Collapse Ratio:"],
],
],
["Hex", "Hexahedron", [["QualityMeasureToEdgeRatio", " Edge Ratio:"]]],
]
if ug.GetNumberOfCells() > 0:
res = ""
for meshType in meshTypes:
if meshType[0] == "Tet":
res += "\n%s%s\n %s" % ("Tetrahedral", " quality of the mesh:", mr.GetFileName())
elif meshType[0] == "Hex":
res += "\n%s%s\n %s" % ("Hexahedral", " quality of the mesh:", mr.GetFileName())
else:
res += "\n%s%s\n %s" % (meshType[1], " quality of the mesh:", mr.GetFileName())
for measure in meshType[2]:
eval("iq.Set" + meshType[0] + measure[0] + "()")
iq.Update()
res += "\n%s\n%s" % (measure[1], DumpQualityStats(iq, "Mesh " + meshType[1] + " Quality"))
res += "\n"
print(res)