def gradient(narray, dataset=None):
"Returns the gradient of an array of scalars/vectors."
if not dataset: dataset = narray.DataSet
if not dataset: raise RuntimeError('Need a dataset to compute gradient')
try:
ncomp = narray.shape[1]
except IndexError:
ncomp = 1
if ncomp != 1 and ncomp != 3:
raise RuntimeError('Gradient only works with scalars (1 component) and vectors (3 component)' +
' Input shape ' + str(narray.shape))
cd = vtk.vtkCellDerivatives()
if ncomp == 1 : attribute_type = 'scalars'
else : attribute_type = 'vectors'
res = _cell_derivatives(narray, dataset, attribute_type, cd)
if ncomp == 1 : retVal = res.GetVectors()
else : retVal = res.GetTensors()
try:
if narray.GetName() : retVal.SetName("gradient of " + narray.GetName())
else : retVal.SetName("gradient")
except AttributeError : retVal.SetName("gradient")
ans = dsa.vtkDataArrayToVTKArray(retVal, dataset)
# The association information has been lost over the vtk filter
# we must reconstruct it otherwise lower pipeline will be broken.
ans.Association = narray.Association
return ans
def gradient(narray, dataset=None):
"Returns the gradient of an array of scalars/vectors."
if not dataset: dataset = narray.DataSet
if not dataset: raise RuntimeError, 'Need a dataset to compute gradient'
try:
ncomp = narray.shape[1]
except IndexError:
ncomp = 1
if ncomp != 1 and ncomp != 3:
raise RuntimeError, 'Gradient only works with scalars (1 component) and vectors (3 component)'\
'Input shape ' + narray.shape
cd = vtk.vtkCellDerivatives()
if ncomp == 1 : attribute_type = 'scalars'
else : attribute_type = 'vectors'
res = _cell_derivatives(narray, dataset, attribute_type, cd)
if ncomp == 1 : retVal = res.GetVectors()
else : retVal = res.GetTensors()
try:
if narray.GetName() : retVal.SetName("gradient of " + narray.GetName())
else : retVal.SetName("gradient")
except AttributeError : retVal.SetName("gradient")
ans = dsa.vtkDataArrayToVTKArray(retVal, dataset)
# The association information has been lost over the vtk filter
# we must reconstruct it otherwise lower pipeline will be broken.
ans.Association = narray.Association
return ans
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
vtk.vtkCellDerivatives(), 'Processing.',
('vtkDataSet',), ('vtkDataSet',),
replaceDoc=True,
inputFunctions=None, outputFunctions=None)
def VtuFieldGradient(inputVtu, fieldName):
"""
Return the gradient of a scalar field in a vtu
"""
tempVtu = vtu()
# Add the points
tempVtu.ugrid.SetPoints(inputVtu.ugrid.GetPoints())
# Add the cells
tempVtu.ugrid.SetCells(inputVtu.ugrid.GetCellTypesArray(), inputVtu.ugrid.GetCellLocationsArray(), inputVtu.ugrid.GetCells())
# Add the field
tempVtu.AddField(fieldName, inputVtu.GetScalarField(fieldName))
tempVtu.ugrid.GetPointData().SetActiveScalars(fieldName)
gradientFilter = vtk.vtkCellDerivatives()
gradientFilter.SetInput(tempVtu.ugrid)
gradientFilter.Update()
projectionFilter = vtk.vtkCellDataToPointData()
projectionFilter.SetInputConnection(gradientFilter.GetOutputPort())
projectionFilter.Update()
tempVtu = vtu()
tempVtu.ugrid = PolyDataToUnstructuredGrid(projectionFilter.GetOutput())
return tempVtu.GetField(tempVtu.GetFieldNames()[-1])
def GetDerivative(self, name):
"""
Returns the derivative of field 'name', a
vector field if 'name' is scalar, and a tensor field
if 'name' is a vector. The field 'name' has to be point-wise data.
The returned array gives a cell-wise derivative.
"""
cd=vtk.vtkCellDerivatives()
cd.SetInput(self.ugrid)
pointdata=self.ugrid.GetPointData()
nc=pointdata.GetArray(name).GetNumberOfComponents()
if nc==1:
cd.SetVectorModeToComputeGradient()
cd.SetTensorModeToPassTensors()
pointdata.SetActiveScalars(name)
cd.Update()
vtkdata=cd.GetUnstructuredGridOutput().GetCellData().GetArray('ScalarGradient')
return arr([vtkdata.GetTuple3(i) for i in range(vtkdata.GetNumberOfTuples())])
else:
cd.SetTensorModeToComputeGradient()
cd.SetVectorModeToPassVectors()
pointdata.SetActiveVectors(name)
cd.Update()
vtkdata=cd.GetUnstructuredGridOutput().GetCellData().GetArray('VectorGradient')
return arr([vtkdata.GetTuple9(i) for i in range(vtkdata.GetNumberOfTuples())])
def strain(narray, dataset=None):
"Returns the strain of an array of 3D vectors."
if not dataset:
dataset = narray.DataSet
if not dataset:
raise RuntimeError("Need a dataset to compute strain")
if 2 != narray.ndim or 3 != narray.shape[1]:
raise RuntimeError("strain only works with an array of 3D vectors" + "Input shape " + str(narray.shape))
cd = vtk.vtkCellDerivatives()
cd.SetTensorModeToComputeStrain()
res = _cell_derivatives(narray, dataset, "vectors", cd)
retVal = res.GetTensors()
retVal.SetName("strain")
ans = dsa.vtkDataArrayToVTKArray(retVal, dataset)
# The association information has been lost over the vtk filter
# we must reconstruct it otherwise lower pipeline will be broken.
ans.Association = narray.Association
return ans
def GetDerivative(self, name):
"""
Returns the derivative of field 'name', a
vector field if 'name' is scalar, and a tensor field
if 'name' is a vector. The field 'name' has to be point-wise data.
The returned array gives a cell-wise derivative.
"""
cd=vtk.vtkCellDerivatives()
cd.SetInputData(self.ugrid)
pointdata=self.ugrid.GetPointData()
nc=pointdata.GetArray(name).GetNumberOfComponents()
if nc==1:
cd.SetVectorModeToComputeGradient()
cd.SetTensorModeToPassTensors()
pointdata.SetActiveScalars(name)
cd.Update()
vtkdata=cd.GetUnstructuredGridOutput().GetCellData().GetArray('ScalarGradient')
return arr([vtkdata.GetTuple3(i) for i in range(vtkdata.GetNumberOfTuples())])
else:
cd.SetTensorModeToComputeGradient()
cd.SetVectorModeToPassVectors()
pointdata.SetActiveVectors(name)
cd.Update()
vtkdata=cd.GetUnstructuredGridOutput().GetCellData().GetArray('VectorGradient')
return arr([vtkdata.GetTuple9(i) for i in range(vtkdata.GetNumberOfTuples())])
def VtuFieldGradient(inputVtu, fieldName):
"""
Return the gradient of a scalar field in a vtu
"""
tempVtu = vtu()
# Add the points
tempVtu.ugrid.SetPoints(inputVtu.ugrid.GetPoints())
# Add the cells
tempVtu.ugrid.SetCells(inputVtu.ugrid.GetCellTypesArray(),
inputVtu.ugrid.GetCellLocationsArray(),
inputVtu.ugrid.GetCells())
# Add the field
tempVtu.AddField(fieldName, inputVtu.GetScalarField(fieldName))
tempVtu.ugrid.GetPointData().SetActiveScalars(fieldName)
gradientFilter = vtk.vtkCellDerivatives()
gradientFilter.SetInput(tempVtu.ugrid)
gradientFilter.Update()
projectionFilter = vtk.vtkCellDataToPointData()
projectionFilter.SetInputConnection(gradientFilter.GetOutputPort())
projectionFilter.Update()
tempVtu = vtu()
tempVtu.ugrid = PolyDataToUnstructuredGrid(projectionFilter.GetOutput())
return tempVtu.GetField(tempVtu.GetFieldNames()[-1])
def initialize (self):
debug ("In Vorticity::initialize()")
self.fil = vtk.vtkCellDerivatives ()
self.fil.SetVectorModeToComputeVorticity ()
self.fil.SetInput(self.prev_fil.GetOutput ())
self.fil.Update ()
self.dimension_to_allow = Tkinter.IntVar ()
self.dimension_to_allow.set (-1)
self.vector_name = Tkinter.StringVar ()
self.vector_name.set ("Vorticity")
def GetVorticity(self, name):
"""
Returns the vorticity of vectorfield 'name'.
The field 'name' has to be point-wise data.
The returned array gives a cell-wise derivative.
"""
cd=vtk.vtkCellDerivatives()
cd.SetInput(self.ugrid)
pointdata=self.ugrid.GetPointData()
cd.SetVectorModeToComputeVorticity()
cd.SetTensorModeToPassTensors()
pointdata.SetActiveVectors(name)
cd.Update()
vtkdata=cd.GetUnstructuredGridOutput().GetCellData().GetArray('VectorGradient')
return arr([vtkdata.GetTuple3(i) for i in range(vtkdata.GetNumberOfTuples())])
def GetVorticity(self, name):
"""
Returns the vorticity of vectorfield 'name'.
The field 'name' has to be point-wise data.
The returned array gives a cell-wise derivative.
"""
cd=vtk.vtkCellDerivatives()
cd.SetInputData(self.ugrid)
pointdata=self.ugrid.GetPointData()
cd.SetVectorModeToComputeVorticity()
cd.SetTensorModeToPassTensors()
pointdata.SetActiveVectors(name)
cd.Update()
vtkdata=cd.GetUnstructuredGridOutput().GetCellData().GetArray('VectorGradient')
return arr([vtkdata.GetTuple3(i) for i in range(vtkdata.GetNumberOfTuples())])
def addDeformationGradients(mesh,
disp_array_name="Displacement",
defo_grad_array_name="DeformationGradient",
verbose=0):
mypy.my_print(verbose, "*** addDeformationGradients ***")
mypy.my_print(
min(verbose, 1),
"*** Warning: at some point the ordering of vector gradient components has changed, and uses C ordering instead of F. ***"
)
if (vtk.vtkVersion.GetVTKMajorVersion() >= 8):
ordering = "C"
elif (vtk.vtkVersion.GetVTKMajorVersion()
== 7) and ((vtk.vtkVersion.GetVTKMinorVersion() > 0) or
(vtk.vtkVersion.GetVTKBuildVersion() > 0)):
ordering = "C"
else:
ordering = "F"
n_cells = mesh.GetNumberOfCells()
assert (mesh.GetPointData().HasArray(disp_array_name))
mesh.GetPointData().SetActiveVectors(disp_array_name)
cell_derivatives = vtk.vtkCellDerivatives()
cell_derivatives.SetVectorModeToPassVectors()
cell_derivatives.SetTensorModeToComputeGradient()
if (vtk.vtkVersion.GetVTKMajorVersion() >= 6):
cell_derivatives.SetInputData(mesh)
else:
cell_derivatives.SetInput(mesh)
cell_derivatives.Update()
farray_gu = cell_derivatives.GetOutput().GetCellData().GetArray(
"VectorGradient")
farray_defo_grad = myvtk.createFloatArray(name=defo_grad_array_name,
n_components=9,
n_tuples=n_cells)
mesh.GetCellData().AddArray(farray_defo_grad)
I = numpy.eye(3)
for k_cell in range(n_cells):
GU = numpy.reshape(farray_gu.GetTuple(k_cell), (3, 3), order=ordering)
F = I + GU
farray_defo_grad.SetTuple(k_cell, numpy.reshape(F, 9, order='C'))
def addDeformationGradients(
mesh,
disp_array_name="Displacement",
defo_grad_array_name="DeformationGradient",
verbose=0):
mypy.my_print(verbose, "*** addDeformationGradients ***")
mypy.my_print(min(verbose,1), "*** Warning: at some point the ordering of vector gradient components has changed, and uses C ordering instead of F. ***")
if (vtk.vtkVersion.GetVTKMajorVersion() >= 8):
ordering = "C"
elif (vtk.vtkVersion.GetVTKMajorVersion() == 7) and ((vtk.vtkVersion.GetVTKMinorVersion() > 0) or (vtk.vtkVersion.GetVTKBuildVersion() > 0)):
ordering = "C"
else:
ordering = "F"
n_cells = mesh.GetNumberOfCells()
assert (mesh.GetPointData().HasArray(disp_array_name))
mesh.GetPointData().SetActiveVectors(disp_array_name)
cell_derivatives = vtk.vtkCellDerivatives()
cell_derivatives.SetVectorModeToPassVectors()
cell_derivatives.SetTensorModeToComputeGradient()
if (vtk.vtkVersion.GetVTKMajorVersion() >= 6):
cell_derivatives.SetInputData(mesh)
else:
cell_derivatives.SetInput(mesh)
cell_derivatives.Update()
farray_gu = cell_derivatives.GetOutput().GetCellData().GetArray("VectorGradient")
farray_defo_grad = myvtk.createFloatArray(
name=defo_grad_array_name,
n_components=9,
n_tuples=n_cells)
mesh.GetCellData().AddArray(farray_defo_grad)
I = numpy.eye(3)
for k_cell in range(n_cells):
GU = numpy.reshape(farray_gu.GetTuple(k_cell), (3,3), order=ordering)
F = I + GU
farray_defo_grad.SetTuple(k_cell, numpy.reshape(F, 9, order='C'))
def curl (narray, dataset=None):
"Returns the curl of an array of 3D vectors."
if not dataset : dataset = narray.DataSet
if not dataset : raise RuntimeError('Need a dataset to compute curl.')
if narray.ndim != 2 or narray.shape[1] != 3 :
raise RuntimeError('Curl only works with an array of 3D vectors.' +
'Input shape ' + str(narray.shape))
cd = vtk.vtkCellDerivatives()
cd.SetVectorModeToComputeVorticity()
res = _cell_derivatives(narray, dataset, 'vectors', cd)
retVal = res.GetVectors()
retVal.SetName("vorticity")
ans = dsa.vtkDataArrayToVTKArray(retVal, dataset)
# The association information has been lost over the vtk filter
# we must reconstruct it otherwise lower pipeline will be broken.
ans.Association = narray.Association
return ans
def strain (narray, dataset=None) :
"Returns the strain of an array of 3D vectors."
if not dataset : dataset = narray.DataSet
if not dataset : raise RuntimeError('Need a dataset to compute strain')
if 2 != narray.ndim or 3 != narray.shape[1] :
raise RuntimeError('strain only works with an array of 3D vectors' +
'Input shape ' + str(narray.shape))
cd = vtk.vtkCellDerivatives()
cd.SetTensorModeToComputeStrain()
res = _cell_derivatives(narray, dataset, 'vectors', cd)
retVal = res.GetTensors()
retVal.SetName("strain")
ans = dsa.vtkDataArrayToVTKArray(retVal, dataset)
# The association information has been lost over the vtk filter
# we must reconstruct it otherwise lower pipeline will be broken.
ans.Association = narray.Association
return ans
def curl (narray, dataset=None):
"Returns the curl of an array of 3D vectors."
if not dataset : dataset = narray.DataSet
if not dataset : raise RuntimeError, 'Need a dataset to compute curl.'
if narray.ndim != 2 or narray.shape[1] != 3 :
raise RuntimeError, 'Curl only works with an array of 3D vectors.'\
'Input shape ' + narray.shape
cd = vtk.vtkCellDerivatives()
cd.SetVectorModeToComputeVorticity()
res = _cell_derivatives(narray, dataset, 'vectors', cd)
retVal = res.GetVectors()
retVal.SetName("vorticity")
ans = dsa.vtkDataArrayToVTKArray(retVal, dataset)
# The association information has been lost over the vtk filter
# we must reconstruct it otherwise lower pipeline will be broken.
ans.Association = narray.Association
return ans
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 deformableRegistration(self):
"""
Performs deformable image registration on images reconstructed from polygonal surfaces at a user-specified precision.
If **animate** parameter is *True*, this also spawns a VTK interative rendering that can animate the deformation.
Returns
-------
cell_fields
"""
for r, mesh in enumerate(self.rmeshes):
print(("Performing deformable image registration for object {:d}"
.format(r + 1)))
rimg, dimg, rpoly = self._poly2img(r)
origin = rimg.GetOrigin()
rimg.SetOrigin((0, 0, 0))
dimg.SetOrigin((0, 0, 0))
steplength = np.min(dimg.GetSpacing()) * 5.0
rimg = sitk.AntiAliasBinary(rimg)
dimg = sitk.AntiAliasBinary(dimg)
#peform the deformable registration
register = sitk.FastSymmetricForcesDemonsRegistrationFilter()
register.SetNumberOfIterations(
self.deformableSettings['Iterations'])
register.SetMaximumRMSError(self.deformableSettings['Maximum RMS'])
register.SmoothDisplacementFieldOn()
register.SetStandardDeviations(
self.deformableSettings['Displacement Smoothing'])
register.SmoothUpdateFieldOff()
register.UseImageSpacingOn()
register.SetMaximumUpdateStepLength(steplength)
register.SetUseGradientType(0)
disp_field = register.Execute(rimg, dimg)
print(("...Elapsed iterations: {:d}"
.format(register.GetElapsedIterations())))
print(("...Change in RMS error: {:6.3f}"
.format(register.GetRMSChange())))
disp_field.SetOrigin(origin)
#translate displacement field to VTK regular grid
a = sitk.GetArrayFromImage(disp_field)
disp = vtk.vtkImageData()
disp.SetOrigin(disp_field.GetOrigin())
disp.SetSpacing(disp_field.GetSpacing())
disp.SetDimensions(disp_field.GetSize())
arr = numpy_to_vtk(a.ravel(), deep=True, array_type=vtk.VTK_DOUBLE)
arr.SetNumberOfComponents(3)
arr.SetName("Displacement")
disp.GetPointData().SetVectors(arr)
#calculate the strain from displacement field
getStrain = vtk.vtkCellDerivatives()
getStrain.SetInputData(disp)
getStrain.SetTensorModeToComputeStrain()
getStrain.Update()
#add the strain tensor to the displacement field structured grid
strains = getStrain.GetOutput()
c2p = vtk.vtkCellDataToPointData()
c2p.PassCellDataOff()
c2p.SetInputData(strains)
c2p.Update()
disp = c2p.GetOutput()
#use VTK probe filter to interpolate displacements and strains
#to 3D meshes of cells and save as UnstructuredGrid (.vtu)
# to visualize in ParaView; this is a linear interpolation
print("...Interpolating displacements to 3D mesh.")
if self.rigidInitial:
#transform 3D Mesh
tf = vtk.vtkTransformFilter()
tf.SetInputData(mesh)
tf.SetTransform(self.rigidTransforms[r])
tf.Update()
mesh = tf.GetOutput()
probe = vtk.vtkProbeFilter()
probe.SetInputData(mesh)
probe.SetSourceData(disp)
probe.Update()
field = probe.GetOutput()
if self.display:
probe2 = vtk.vtkProbeFilter()
probe2.SetInputData(rpoly)
probe2.SetSourceData(disp)
probe2.Update()
self.cell_fields.append(field)
if self.saveFEA:
idisp = field.GetPointData().GetVectors()
bcs = np.zeros((len(self._snodes[r]), 3), float)
for j, node in enumerate(self._snodes[r]):
d = idisp.GetTuple3(node - 1)
bcs[j, 0] = d[0]
bcs[j, 1] = d[1]
bcs[j, 2] = d[2]
self._bcs.append(bcs)
idWriter = vtk.vtkXMLUnstructuredGridWriter()
idWriter.SetFileName(
str(os.path.normpath(self._def_dir + os.sep +
'cell{:04d}.vtu'.format(r + 1))))
idWriter.SetInputData(self.cell_fields[r])
idWriter.Write()
if self.display:
self.animate(probe2.GetOutput(), r)
print("Registration completed.")
locals()[get_variable_name("", cell, "Scalar")].SetValue(i, 0)
i = i + 1
locals()[get_variable_name("", cell, "Scalar")].SetValue(0, 4)
locals()[get_variable_name("", cell, "Grid")].GetPointData().SetScalars(
locals()[get_variable_name("", cell, "Scalar")])
pass
# write to the temp directory if possible, otherwise use .
dir = "."
if (info.commands(globals(), locals(), "rtTester") == "rtTester"):
dir = rtTester.GetTempDirectory()
pass
for cell in "aVoxel aHexahedron aWedge aPyramid aTetra aQuad aTriangle aTriangleStrip aLine aPolyLine aVertex aPolyVertex aPixel aPolygon aPenta aHexa".split(
):
locals()[get_variable_name("", cell, "derivs")] = vtk.vtkCellDerivatives()
locals()[get_variable_name("", cell, "derivs")].SetInputData(
locals()[get_variable_name("", cell, "Grid")])
locals()[get_variable_name("", cell,
"derivs")].SetVectorModeToComputeGradient()
FileName = dir
FileName += cell
FileName += ".vtk"
# make sure the directory is writeable first
if (catch.catch(
globals(),
"""channel = open("" + str(dir) + "/test.tmp", "w")""") == 0):
channel.close()
file.delete("-force", "" + str(dir) + "/test.tmp")
locals()[get_variable_name(
"", cell, "Writer")] = vtk.vtkUnstructuredGridWriter()
def main(argv):
try:
opts, args = getopt.getopt(argv,"hi:o:x:a:y:b:z:c:d:u:", ["ifile=","ofile=","sx=","ex=","sy=","ez=","dataset=","comp="])
except getopt.GetoptError as err:
print 'getmultithresh.py -i <inputfile.h5> -o <outputfile.vti> -sx -ex -sy -ey -sz -ez -dataset -comptype'
print (str(err))
for opt, arg in opts:
if opt == '-h':
print 'getmultithresh.py -i <inputfile.h5> -o <outputfile.vti> -sx -ex -sy -ey -sz -ez -dataset'
sys.exit()
elif opt in ("-i", "--ifile"):
inputfile = arg
elif opt in ("-o", "--ofile"):
outputfile = arg
elif opt in ("-x", "--sx"):
sx = int(arg)
elif opt in ("-a", "--ex"):
ex = int(arg)
elif opt in ("-y", "--sy"):
sy = int(arg)
elif opt in ("-b", "--ey"):
ey = int(arg)
elif opt in ("-z", "--sz"):
sz = int(arg)
elif opt in ("-c", "--ez"):
ez = int(arg)
elif opt in ("-d", "--dataset"):
dataset = str(arg)
elif opt in ("-u", "--du"):
comptype = str(arg)
print ("Loading file, %s" % inputfile)
#Determine if file is h5 or numpy
if (inputfile.split(".")[1] == "npy"):
rs = timeit.default_timer()
vel = np.load(inputfile)
re = timeit.default_timer()
else:
#read in file
rs = timeit.default_timer()
data_file = h5py.File(inputfile, 'r')
vel = np.array(data_file[dataset])
data_file.close()
re = timeit.default_timer()
cs = timeit.default_timer()
#convert numpy array to vtk
vtkdata = numpy_support.numpy_to_vtk(vel.flat, deep=True, array_type=vtk.VTK_FLOAT)
vtkdata.SetNumberOfComponents(3)
vtkdata.SetName("Velocity")
image = vtk.vtkImageData()
image.GetPointData().SetVectors(vtkdata)
image.SetExtent(sx,ex,sy,ey,sz,ez)
#NOTE: Hardcoding Spacing
image.SetSpacing(.006135923, .006135923, .006135923)
print ("Doing computation")
ce = timeit.default_timer()
vs = timeit.default_timer()
ve = timeit.default_timer()
print ("Generating contour")
ms = timeit.default_timer()
mag = vtk.vtkImageMagnitude()
for x in range (0,1):
start = timeit.default_timer()
threshold = (22.39 * (2.5))
if (comptype == "q"):
threshold= (783.3)
vort = vtk.vtkGradientFilter()
vort.SetInputData(image)
vort.SetInputScalars(image.FIELD_ASSOCIATION_POINTS,"Velocity")
vort.ComputeQCriterionOn()
vort.Update()
image.GetPointData().SetScalars(vort.GetOutput().GetPointData().GetVectors("Q-criterion"))
else:
v = vtk.vtkCellDerivatives()
v.SetVectorModeToComputeVorticity()
v.SetTensorModeToPassTensors()
v.SetInputData(image)
v.Update()
vort = vtk.vtkImageMagnitude()
cp = vtk.vtkCellDataToPointData()
cp.SetInputData(v.GetOutput())
cp.Update()
image.GetPointData().SetScalars(cp.GetOutput().GetPointData().GetVectors())
vort.SetInputData(image)
vort.Update()
#ni = vtk.vtkImageData()
#ni.SetSpacing(.006135923, .006135923, .006135923)
#ni.SetExtent(sx,ex,sy,ey,sz,ez)
#ni.GetPointData().SetScalars(q.GetOutput().GetPointData().GetVectors("Q-criterion"))
mend = timeit.default_timer()
me = mend
comptime = mend-start
print("Magnitude Computation time: " + str(comptime) + "s")
c = vtk.vtkContourFilter()
c.SetValue(0,threshold)
if (comptype == "q"):
c.SetInputData(image)
else:
c.SetInputData(vort.GetOutput())
print("Computing Contour with threshold", threshold)
c.Update()
w = vtk.vtkXMLPolyDataWriter()
w.SetEncodeAppendedData(0) #turn of base 64 encoding for fast write
w.SetFileName(outputfile + str(x) + ".vtp ")
w.SetInputData(c.GetOutput())
ws = timeit.default_timer()
w.Write()
we = timeit.default_timer()
print("Results:")
print("Read time: %s" % str(re-rs))
print ("Convert to vtk: %s" % str(ce-cs))
if (comptype == "q"):
print ("Q Computation: %s" % str(ve-vs))
print ("Q Magnitude: %s" % str(me-ms))
else:
print ("Vorticity Computation: %s" % str(ve-vs))
print ("Vorticity Magnitude: %s" % str(me-ms))
#print ("Threshold: %s" % str(te-ts))
print ("Write %s" % str(we-ws))
print ("Total time: %s" % str(we-rs))
i = 0
while i < N:
locals()[get_variable_name("", cell, "Scalar")].SetValue(i,0)
i = i + 1
locals()[get_variable_name("", cell, "Scalar")].SetValue(0,4)
locals()[get_variable_name("", cell, "Grid")].GetPointData().SetScalars(locals()[get_variable_name("", cell, "Scalar")])
pass
# write to the temp directory if possible, otherwise use .
dir = "."
if (info.commands(globals(), locals(), "rtTester") == "rtTester"):
dir = rtTester.GetTempDirectory()
pass
for cell in "aVoxel aHexahedron aWedge aPyramid aTetra aQuad aTriangle aTriangleStrip aLine aPolyLine aVertex aPolyVertex aPixel aPolygon aPenta aHexa".split():
locals()[get_variable_name("", cell, "derivs")] = vtk.vtkCellDerivatives()
locals()[get_variable_name("", cell, "derivs")].SetInputData(locals()[get_variable_name("", cell, "Grid")])
locals()[get_variable_name("", cell, "derivs")].SetVectorModeToComputeGradient()
FileName = dir
FileName += cell
FileName += ".vtk"
# make sure the directory is writeable first
if (catch.catch(globals(),"""channel = open("" + str(dir) + "/test.tmp", "w")""") == 0):
channel.close()
file.delete("-force", "" + str(dir) + "/test.tmp")
locals()[get_variable_name("", cell, "Writer")] = vtk.vtkUnstructuredGridWriter()
locals()[get_variable_name("", cell, "Writer")].SetInputConnection(locals()[get_variable_name("", cell, "derivs")].GetOutputPort())
locals()[get_variable_name("", cell, "Writer")].SetFileName(FileName)
locals()[get_variable_name("", cell, "Writer")].Write()
# delete the file
file.delete("-force", FileName)
import vtk
print vtk.VTK_VERSION
r = vtk.vtkXMLImageDataReader()
r.SetFileName("iso0_67.vti")
r.Update()
image = r.GetOutput()
vorticity = vtk.vtkCellDerivatives()
vorticity.SetVectorModeToComputeVorticity()
vorticity.SetTensorModeToPassTensors()
vorticity.SetInputData(image)
vorticity.Update()
mag = vtk.vtkImageMagnitude()
cp = vtk.vtkCellDataToPointData()
cp.SetInputData(vorticity.GetOutput())
cp.Update()
image.GetPointData().SetScalars(cp.GetOutput().GetPointData().GetVectors())
mag.SetInputData(image)
mag.Update()
#Remove velocity field
#m = mag.GetOutput()
#m.GetPointData().RemoveArray("Velocity")
t = vtk.vtkImageThreshold()
t.SetInputData(mag.GetOutput())
t.SetInputArrayToProcess(0, 0, 0,
mag.GetOutput().FIELD_ASSOCIATION_POINTS, "Magnitude")
def getvtkimage(self, webargs, timestep):
#Setup query
DBSTRING = os.environ['db_connection_string']
conn = pyodbc.connect(DBSTRING, autocommit=True)
cursor = conn.cursor()
#url = "http://localhost:8000/cutout/getcutout/"+ token + "/" + dataset + "/" + datafield + "/" + ts + "," +te + "/" + xs + "," + xe +"/" + ys + "," + ye +"/" + zs + "," + ze
w = webargs.split("/")
ts = int(w[3].split(',')[0])
te = int(w[3].split(',')[1])
xs = int(w[4].split(',')[0])
xe = int(w[4].split(',')[1])
ys = int(w[5].split(',')[0])
ye = int(w[5].split(',')[1])
zs = int(w[6].split(',')[0])
ze = int(w[6].split(',')[1])
extent = (xs, ys, zs, xe, ye, ze)
overlap = 2 #Used only on contours--vorticity and Q-criterion
#Look for step parameters
if (len(w) > 9):
step = True;
s = w[8].split(",")
tstep = s[0]
xstep = float(s[1])
ystep = float(s[2])
zstep = float(s[3])
filterwidth = w[9]
else:
step = False;
xstep = 1
ystep = 1
zstep = 1
filterwidth = 1
cfieldlist = w[2].split(",")
firstval = cfieldlist[0]
maxrange = self.getmaxrange(w[1])
if ((firstval == 'vo') or (firstval == 'qc') or (firstval == 'cvo') or (firstval == 'qcc')):
component = 'u'
computation = firstval #We are doing a computation, so we need to know which one.
#check to see if we have a threshold (only for contours)
if (len(cfieldlist) > 1):
threshold = float(cfieldlist[1])
else:
threshold = .6
#New: We need an expanded cutout if contouring. Push the cutout out by 2 in all directions (unless at boundary).
if ((firstval == 'cvo') or (firstval == 'qcc')):
newextent = self.expandcutout(extent, maxrange[0], maxrange[1], maxrange[2], overlap)
contour = True
else:
component = w[2] #There could be multiple components, so we will have to loop
computation = ''
#Split component into list and add them to the image
#Check to see if we have a value for vorticity or q contour
fieldlist = list(component)
for field in fieldlist:
print("Field = %s" % field)
cursor.execute("{CALL turbdev.dbo.GetAnyCutout(?,?,?,?,?,?,?,?,?,?,?,?,?,?,?,?)}",w[1], field, timestep, extent[0], extent[1], extent[2], xstep, ystep, zstep, 1,1,extent[3], extent[4], extent[5],filterwidth,1)
#If data spans across multiple servers, we get multiple sets, so concatenate them.
row = cursor.fetchone()
raw = row[0]
part = 0
print ("First part size is %d" % len(row[0]))
while(cursor.nextset()):
row = cursor.fetchone()
raw = raw + row[0]
part = part +1
print ("added part %d" % part)
print ("Part size is %d" % len(row[0]))
print ("Raw size is %d" % len(raw))
data = np.frombuffer(raw, dtype=np.float32)
conn.close()
vtkdata = numpy_support.numpy_to_vtk(data, deep=True, array_type=vtk.VTK_FLOAT)
components = self.numcomponents(field)
vtkdata.SetNumberOfComponents(components)
vtkdata.SetName(self.componentname(field))
image = vtk.vtkImageData()
if (step):
xes = int(extent[3])/int(xstep)-1
yes = int(extent[4])/int(ystep)-1
zes = int(extent[5])/int(zstep)-1
image.SetExtent(extent[0], extent[0]+extent[3], extent[1], extent[1]+extent[4], extent[2], extenet[2]+extenet[5])
print("Step extent=" +str(xes))
print("xs=" + str(xstep) + " ys = "+ str(ystep) +" zs = " + str(zstep))
else:
image.SetExtent(extent[0], extent[0]+extent[3]-1, extent[1], extent[1]+extent[4]-1, extent[2], extent[2]+extent[5]-1)
image.GetPointData().SetVectors(vtkdata)
if (step): #Magnify to original size
image.SetSpacing(xstep,ystep,zstep)
#Check if we need a rectilinear grid, and set it up if so.
if (w[1] == 'channel'):
ygrid = self.getygrid()
#print("Ygrid: ")
#print (ygrid)
rg = vtk.vtkRectilinearGrid()
#Not sure about contouring channel yet, so we are going back to original variables at this point.
rg.SetExtent(xs, xs+xe-1, ys, ys+ye-1, zs, zs+ze-1)
rg.GetPointData().SetVectors(vtkdata)
xg = np.arange(float(xs),float(xe))
zg = np.arange(float(zs),float(ze))
for x in xg:
xg[x] = 8*3.141592654/2048*x
for z in zg:
zg[z] = 3*3.141592654/2048*z
vtkxgrid=numpy_support.numpy_to_vtk(xg, deep=True,
array_type=vtk.VTK_FLOAT)
vtkzgrid=numpy_support.numpy_to_vtk(zg, deep=True,
array_type=vtk.VTK_FLOAT)
vtkygrid=numpy_support.numpy_to_vtk(ygrid,
deep=True, array_type=vtk.VTK_FLOAT)
rg.SetXCoordinates(vtkxgrid)
rg.SetZCoordinates(vtkzgrid)
rg.SetYCoordinates(vtkygrid)
image = rg #we rewrite the image since we may be doing a
#computation below
#See if we are doing a computation
if (computation == 'vo'):
vorticity = vtk.vtkCellDerivatives()
vorticity.SetVectorModeToComputeVorticity()
vorticity.SetTensorModeToPassTensors()
vorticity.SetInputData(image)
print("Computing Vorticity")
vorticity.Update()
elif (computation == 'cvo'):
vorticity = vtk.vtkCellDerivatives()
vorticity.SetVectorModeToComputeVorticity()
vorticity.SetTensorModeToPassTensors()
vorticity.SetInputData(image)
print("Computing Voricity")
vorticity.Update()
mag = vtk.vtkImageMagnitude()
cp = vtk.vtkCellDataToPointData()
cp.SetInputData(vorticity.GetOutput())
print("Computing magnitude")
cp.Update()
image.GetPointData().SetScalars(cp.GetOutput().GetPointData().GetVectors())
mag.SetInputData(image)
mag.Update()
c = vtk.vtkContourFilter()
c.SetValue(0,threshold)
c.SetInputData(mag.GetOutput())
print("Computing Contour")
c.Update()
#Now we need to clip out the overlap
box = vtk.vtkBox()
#set box to requested size
box.SetBounds(xs, xs+xe-1, ys, ys+ye-1, zs,zs+ze-1)
clip = vtk.vtkClipPolyData()
clip.SetClipFunction(box)
clip.GenerateClippedOutputOn()
clip.SetInputData(c.GetOutput())
clip.InsideOutOn()
clip.Update()
cropdata = clip.GetOutput()
return cropdata
elif (computation == 'qcc'):
q = vtk.vtkGradientFilter()
q.SetInputData(image)
q.SetInputScalars(image.FIELD_ASSOCIATION_POINTS,"Velocity")
q.ComputeQCriterionOn()
q.Update()
#newimage = vtk.vtkImageData()
image.GetPointData().SetScalars(q.GetOutput().GetPointData().GetVectors("Q-criterion"))
mag = vtk.vtkImageMagnitude()
mag.SetInputData(image)
mag.Update()
c = vtk.vtkContourFilter()
c.SetValue(0,threshold)
c.SetInputData(mag.GetOutput())
c.Update()
#clip out the overlap here
box = vtk.vtkBox()
#set box to requested size
box.SetBounds(xs, xs+xe-1, ys, ys+ye-1, zs,zs+ze-1)
clip = vtk.vtkClipPolyData()
clip.SetClipFunction(box)
clip.GenerateClippedOutputOn()
clip.SetInputData(c.GetOutput())
clip.InsideOutOn()
clip.Update()
cropdata = clip.GetOutput()
return cropdata
else:
return image
def getvtkdata(self, ci, timestep):
PI= 3.141592654
contour=False
firstval = ci.datafields.split(',')[0]
#print ("First: ", firstval)
if ((firstval == 'vo') or (firstval == 'qc') or (firstval == 'cvo') or (firstval == 'pcvo') or (firstval == 'qcc')):
datafields = 'u'
computation = firstval #We are doing a computation, so we need to know which one.
if ((firstval == 'cvo') or (firstval == 'qcc') or (firstval == 'pcvo')):
overlap = 3 #This was 2, but due to rounding because of the spacing, 3 is required.
#Save a copy of the original request
oci = jhtdblib.CutoutInfo()
oci.xstart = ci.xstart
oci.ystart = ci.ystart
oci.zstart = ci.zstart
oci.xlen = ci.xlen
oci.ylen = ci.ylen
oci.zlen = ci.zlen
ci = self.expandcutout(ci, overlap) #Expand the cutout by the overlap
contour = True
else:
datafields = ci.datafields.split(',') #There could be multiple components, so we will have to loop
computation = ''
#Split component into list and add them to the image
#Check to see if we have a value for vorticity or q contour
fieldlist = list(datafields)
image = vtk.vtkImageData()
rg = vtk.vtkRectilinearGrid()
for field in fieldlist:
if (ci.xlen > 61 and ci.ylen > +61 and ci.zlen > 61 and ci.xstep ==1 and ci.ystep ==1 and ci.zstep ==1 and not contour):
#Do this if cutout is too large
#Note: we don't want to get cubed data if we are doing cubes for contouring.
data=GetData().getcubedrawdata(ci, timestep, field)
else:
data=GetData().getrawdata(ci, timestep, field)
vtkdata = numpy_support.numpy_to_vtk(data.flat, deep=True, array_type=vtk.VTK_FLOAT)
components = Datafield.objects.get(shortname=field).components
vtkdata.SetNumberOfComponents(components)
vtkdata.SetName(Datafield.objects.get(shortname=field).longname)
#We need to see if we need to subtract one on end of extent edges.
image.SetExtent(ci.xstart, ci.xstart+((ci.xlen+ci.xstep-1)/ci.xstep)-1, ci.ystart, ci.ystart+((ci.ylen+ci.ystep-1)/ci.ystep)-1, ci.zstart, ci.zstart+((ci.zlen+ci.zstep-1)/ci.zstep)-1)
#image.SetExtent(ci.xstart, ci.xstart+int(ci.xlen)-1, ci.ystart, ci.ystart+int(ci.ylen)-1, ci.zstart, ci.zstart+int(ci.zlen)-1)
image.GetPointData().AddArray(vtkdata)
if (Datafield.objects.get(shortname=field).longname == "Velocity"):
#Set the Velocity Array as vectors in the image.
image.GetPointData().SetVectors(image.GetPointData().GetArray("Velocity"))
#Get spacing from database and multiply it by the step. Don't do this on the contour--it is performed later on.
#if (contour):
#We need to scale the threshold to the spacing of the dataset. This is because we build the cubes
#on a 1 spacing cube in order to get proper overlap on the contours.
#ci.threshold = ci.threshold*Dataset.objects.get(dbname_text=ci.dataset).xspacing
#else:
xspacing = Dataset.objects.get(dbname_text=ci.dataset).xspacing
yspacing = Dataset.objects.get(dbname_text=ci.dataset).yspacing
zspacing = Dataset.objects.get(dbname_text=ci.dataset).zspacing
#Check if we need a rectilinear grid, and set it up if so.
if (ci.dataset == 'channel'):
ygrid = jhtdblib.JHTDBLib().getygrid()
#print("Ygrid: ")
#print (ygrid)
#Not sure about contouring channel yet, so we are going back to original variables at this point.
rg.SetExtent(ci.xstart, ci.xstart+((ci.xlen+ci.xstep-1)/ci.xstep)-1, ci.ystart, ci.ystart+((ci.ylen+ci.ystep-1)/ci.ystep)-1, ci.zstart, ci.zstart+((ci.zlen+ci.zstep-1)/ci.zstep)-1)
#components = Datafield.objects.get(shortname=field).components
#vtkdata.SetNumberOfComponents(components)
#vtkdata.SetName(Datafield.objects.get(shortname=field).longname)
rg.GetPointData().AddArray(vtkdata)
#import pdb;pdb.set_trace()
#This isn't possible--we will have to do something about this in the future.
#rg.SetSpacing(ci.xstep,ci.ystep,ci.zstep)
xg = np.arange(0,2047.0)
zg = np.arange(0,1535.0)
for x in xg:
xg[x] = 8*PI/2048*x
for z in zg:
zg[z] = 3*PI/2048*z
vtkxgrid=numpy_support.numpy_to_vtk(xg, deep=True,
array_type=vtk.VTK_FLOAT)
vtkzgrid=numpy_support.numpy_to_vtk(zg, deep=True,
array_type=vtk.VTK_FLOAT)
vtkygrid=numpy_support.numpy_to_vtk(ygrid,
deep=True, array_type=vtk.VTK_FLOAT)
rg.SetXCoordinates(vtkxgrid)
rg.SetZCoordinates(vtkzgrid)
rg.SetYCoordinates(vtkygrid)
image = rg #we rewrite the image since we may be doing a
#computation below
else:
image.SetSpacing(xspacing*ci.xstep,yspacing*ci.ystep,zspacing*ci.zstep)
#See if we are doing a computation
if (computation == 'vo'):
start = time.time()
vorticity = vtk.vtkCellDerivatives()
vorticity.SetVectorModeToComputeVorticity()
vorticity.SetTensorModeToPassTensors()
vorticity.SetInputData(image)
#print("Computing Vorticity")
vorticity.Update()
end = time.time()
comptime = end-start
print("Vorticity Computation time: " + str(comptime) + "s")
return image
elif (computation == 'cvo' or computation == 'pcvo'):
start = time.time()
vorticity = vtk.vtkCellDerivatives()
vorticity.SetVectorModeToComputeVorticity()
vorticity.SetTensorModeToPassTensors()
vorticity.SetInputData(image)
#print("Computing Voricity")
vorticity.Update()
vend = time.time()
comptime = vend-start
print("Vorticity Computation time: " + str(comptime) + "s")
mag = vtk.vtkImageMagnitude()
cp = vtk.vtkCellDataToPointData()
cp.SetInputData(vorticity.GetOutput())
#print("Computing magnitude")
cp.Update()
mend = time.time()
image.GetPointData().SetScalars(cp.GetOutput().GetPointData().GetVectors())
mag.SetInputData(image)
mag.Update()
comptime = mend-vend
print("Magnitude Computation time: " + str(comptime) + "s")
c = vtk.vtkContourFilter()
c.SetValue(0,ci.threshold)
c.SetInputData(mag.GetOutput())
print("Computing Contour with threshold", ci.threshold)
c.Update()
cend = time.time()
comptime = cend-mend
print("Contour Computation time: " + str(comptime) + "s")
#Now we need to clip out the overlap
box = vtk.vtkBox()
#set box to requested size
#The OCI deepcopy didn't seem to work. Manually taking the overlap again.
box.SetBounds(oci.xstart*xspacing, (oci.xstart+oci.xlen)*xspacing, oci.ystart*yspacing, (oci.ystart+oci.ylen)*yspacing, oci.zstart*yspacing,(oci.zstart+oci.zlen)*yspacing)
clip = vtk.vtkClipPolyData()
clip.SetClipFunction(box)
clip.GenerateClippedOutputOn()
clip.SetInputData(c.GetOutput())
clip.InsideOutOn()
clip.Update()
#import pdb;pdb.set_trace()
cropdata = clip.GetOutput()
#Cleanup
image.ReleaseData()
#mag.ReleaseData()
#box.ReleaseData()
#clip.ReleaseData()
#image.Delete()
#box.Delete()
#vorticity.Delete()
end = time.time()
comptime = end-start
print("Total Computation time: " + str(comptime) + "s")
#return cropdata
#We need the output port for appending, so return the clip instead
return clip
elif (computation == 'qcc'):
start = time.time()
q = vtk.vtkGradientFilter()
q.SetInputData(image)
q.SetInputScalars(image.FIELD_ASSOCIATION_POINTS,"Velocity")
q.ComputeQCriterionOn()
q.Update()
image.GetPointData().SetScalars(q.GetOutput().GetPointData().GetVectors("Q-criterion"))
#mag = vtk.vtkImageMagnitude()
#mag.SetInputData(image)
#mag.Update()
mend = time.time()
comptime = mend-start
#print("Magnitude Computation time: " + str(comptime) + "s")
c = vtk.vtkContourFilter()
c.SetValue(0,ci.threshold)
c.SetInputData(image)
print("Computing Contour with threshold", ci.threshold)
c.Update()
cend = time.time()
comptime = cend-mend
print("Q Contour Computation time: " + str(comptime) + "s")
#clip out the overlap here
box = vtk.vtkBox()
#set box to requested size
box.SetBounds(oci.xstart, oci.xstart+oci.xlen-1, oci.ystart, oci.ystart+oci.ylen-1, oci.zstart,oci.zstart+oci.zlen-1)
clip = vtk.vtkClipPolyData()
clip.SetClipFunction(box)
clip.GenerateClippedOutputOn()
clip.SetInputData(c.GetOutput())
clip.InsideOutOn()
clip.Update()
cropdata = clip.GetOutput()
end = time.time()
comptime = end-start
print("Computation time: " + str(comptime) + "s")
#return cropdata
return clip
else:
return image
def compute_vonMisesStress_for_MV(inputfilename, outputfilename):
# ======================================================================
# get system arguments -------------------------------------------------
# Path to input file and name of the output file
#inputfilename = sys.argv[1]
#outputfilename = sys.argv[2]
print " "
print "=================================================================================================="
print "=== Execute Python script to analyze MV geometry in order for the HiFlow3-based MVR-Simulation ==="
print "=================================================================================================="
print " "
# ======================================================================
# Read file
if inputfilename[-4] == 'p':
reader = vtk.vtkXMLPUnstructuredGridReader()
reader.SetFileName(inputfilename)
reader.Update()
else:
reader = vtk.vtkXMLUnstructuredGridReader()
reader.SetFileName(inputfilename)
reader.Update()
print "Reading input files: DONE."
# ======================================================================
# Compute displacement vector
calc = vtk.vtkArrayCalculator()
calc.SetInput(reader.GetOutput())
calc.SetAttributeModeToUsePointData()
calc.AddScalarVariable('x', 'u0', 0)
calc.AddScalarVariable('y', 'u1', 0)
calc.AddScalarVariable('z', 'u2', 0)
calc.SetFunction('x*iHat+y*jHat+z*kHat')
calc.SetResultArrayName('DisplacementSolutionVector')
calc.Update()
# ======================================================================
# Compute strain tensor
derivative = vtk.vtkCellDerivatives()
derivative.SetInput(calc.GetOutput())
derivative.SetTensorModeToComputeStrain()
derivative.Update()
# ======================================================================
# Compute von Mises stress
calc = vtk.vtkArrayCalculator()
calc.SetInput(derivative.GetOutput())
calc.SetAttributeModeToUseCellData()
calc.AddScalarVariable('Strain_0', 'Strain', 0)
calc.AddScalarVariable('Strain_1', 'Strain', 1)
calc.AddScalarVariable('Strain_2', 'Strain', 2)
calc.AddScalarVariable('Strain_3', 'Strain', 3)
calc.AddScalarVariable('Strain_4', 'Strain', 4)
calc.AddScalarVariable('Strain_5', 'Strain', 5)
calc.AddScalarVariable('Strain_6', 'Strain', 6)
calc.AddScalarVariable('Strain_7', 'Strain', 7)
calc.AddScalarVariable('Strain_8', 'Strain', 8)
calc.SetFunction('sqrt( (2*700*Strain_0 + 28466*(Strain_0+Strain_4+Strain_8))^2 + (2*700*Strain_4 + 28466*(Strain_0+Strain_4+Strain_8))^2 + (2*700*Strain_8 + 28466*(Strain_0+Strain_4+Strain_8))^2 - ( (2*700*Strain_0 + 28466*(Strain_0+Strain_4+Strain_8))*(2*700*Strain_4 + 28466*(Strain_0+Strain_4+Strain_8)) ) - ( (2*700*Strain_0 + 28466*(Strain_0+Strain_4+Strain_8))*(2*700*Strain_8 + 28466*(Strain_0+Strain_4+Strain_8)) ) - ( (2*700*Strain_4 + 28466*(Strain_0+Strain_4+Strain_8))*(2*700*Strain_8 + 28466*(Strain_0+Strain_4+Strain_8)) ) + 3 * ((2*700*Strain_3)^2 + (2*700*Strain_6)^2 + (2*700*Strain_7)^2) )')
calc.SetResultArrayName('vonMisesStress_forMV_mu700_lambda28466')
calc.Update()
print "Computation of displacement vectors, Cauchy strain and vom Mises stress: DONE."
# ======================================================================
# Define dummy variable; get output of calc filter
dummy = calc.GetOutput()
# Get point data arrays u0, u1 and u2
pointData_u0 = dummy.GetPointData().GetArray('u0')
pointData_u1 = dummy.GetPointData().GetArray('u1')
pointData_u2 = dummy.GetPointData().GetArray('u2')
# Set scalars
dummy.GetPointData().SetScalars(pointData_u0)
# ======================================================================
# Warp by scalar u0
warpScalar = vtk.vtkWarpScalar()
warpScalar.SetInput(dummy)
warpScalar.SetNormal(1.0,0.0,0.0)
warpScalar.SetScaleFactor(1.0)
warpScalar.SetUseNormal(1)
warpScalar.Update()
# Get output and set scalars
dummy = warpScalar.GetOutput()
dummy.GetPointData().SetScalars(pointData_u1)
# ======================================================================
# Warp by scalar u1
warpScalar = vtk.vtkWarpScalar()
warpScalar.SetInput(dummy)
warpScalar.SetNormal(0.0,1.0,0.0)
warpScalar.SetScaleFactor(1.0)
warpScalar.SetUseNormal(1)
warpScalar.Update()
# Get output and set scalars
dummy = warpScalar.GetOutput()
dummy.GetPointData().SetScalars(pointData_u2)
# ======================================================================
# Warp by scalar u2
warpScalar = vtk.vtkWarpScalar()
warpScalar.SetInput(dummy)
warpScalar.SetNormal(0.0,0.0,1.0)
warpScalar.SetScaleFactor(1.0)
warpScalar.SetUseNormal(1)
warpScalar.Update()
# Get ouput and add point data arrays that got deleted earlier
dummy = warpScalar.GetOutput()
dummy.GetPointData().AddArray(pointData_u0)
dummy.GetPointData().AddArray(pointData_u1)
# ======================================================================
# Write output to vtu
writer = vtk.vtkXMLUnstructuredGridWriter()
writer.SetDataModeToAscii()
writer.SetFileName(outputfilename)
writer.SetInput(dummy)
writer.Write()
# ======================================================================
print "Writing Extended VTU incl. von Mises Stress information: DONE."
print "=============================================================="
print " "
import vtk
print vtk.VTK_VERSION
r = vtk.vtkXMLImageDataReader()
r.SetFileName("iso0_67.vti")
r.Update()
image = r.GetOutput()
vorticity = vtk.vtkCellDerivatives()
vorticity.SetVectorModeToComputeVorticity()
vorticity.SetTensorModeToPassTensors()
vorticity.SetInputData(image)
vorticity.Update()
mag = vtk.vtkImageMagnitude()
cp = vtk.vtkCellDataToPointData()
cp.SetInputData(vorticity.GetOutput())
cp.Update()
image.GetPointData().SetScalars(cp.GetOutput().GetPointData().GetVectors())
mag.SetInputData(image)
mag.Update()
#Remove velocity field
#m = mag.GetOutput()
#m.GetPointData().RemoveArray("Velocity")
t = vtk.vtkImageThreshold()
t.SetInputData(mag.GetOutput())
t.SetInputArrayToProcess(0,0,0, mag.GetOutput().FIELD_ASSOCIATION_POINTS, "Magnitude")
#t.ThresholdByUpper(44.79)
def computeStrainsFromDisplacements(
mesh,
disp_array_name="displacement",
ref_mesh=None,
verbose=0):
myVTK.myPrint(verbose, "*** computeStrainsFromDisplacements ***")
myVTK.myPrint(min(verbose,1), "*** Warning: at some point the ordering of vector gradient components has changed, and uses C ordering instead of F. ***")
if (vtk.vtkVersion.GetVTKMajorVersion() >= 8):
ordering = "C"
elif (vtk.vtkVersion.GetVTKMajorVersion() == 7) and ((vtk.vtkVersion.GetVTKMinorVersion() > 0) or (vtk.vtkVersion.GetVTKBuildVersion() > 0)):
ordering = "C"
else:
ordering = "F"
n_points = mesh.GetNumberOfPoints()
n_cells = mesh.GetNumberOfCells()
assert (mesh.GetPointData().HasArray(disp_array_name))
mesh.GetPointData().SetActiveVectors(disp_array_name)
cell_derivatives = vtk.vtkCellDerivatives()
cell_derivatives.SetVectorModeToPassVectors()
cell_derivatives.SetTensorModeToComputeGradient()
if (vtk.vtkVersion.GetVTKMajorVersion() >= 6):
cell_derivatives.SetInputData(mesh)
else:
cell_derivatives.SetInput(mesh)
cell_derivatives.Update()
farray_gu = cell_derivatives.GetOutput().GetCellData().GetArray("VectorGradient")
if (ref_mesh is not None):
farray_strain = myVTK.createFloatArray(
name="Strain_CAR",
n_components=6,
n_tuples=n_cells)
else:
farray_strain = myVTK.createFloatArray(
name="Strain",
n_components=6,
n_tuples=n_cells)
mesh.GetCellData().AddArray(farray_strain)
I = numpy.eye(3)
E_vec = numpy.empty(6)
#e_vec = numpy.empty(6)
for k_cell in range(n_cells):
GU = numpy.reshape(farray_gu.GetTuple(k_cell), (3,3), ordering)
F = I + GU
C = numpy.dot(numpy.transpose(F), F)
E = (C - I)/2
mat_sym33_to_vec_col6(E, E_vec)
farray_strain.SetTuple(k_cell, E_vec)
#if (add_almansi_strain):
#Finv = numpy.linalg.inv(F)
#c = numpy.dot(numpy.transpose(Finv), Finv)
#e = (I - c)/2
#mat_sym33_to_vec_col6(e, e_vec)
#farray_almansi.SetTuple(k_cell, e_vec)
if (ref_mesh is not None) and (ref_mesh.GetCellData().HasArray("eR")) and (ref_mesh.GetCellData().HasArray("eC")) and (ref_mesh.GetCellData().HasArray("eL")):
farray_strain_cyl = myVTK.rotateMatrix(
old_array=mesh.GetCellData().GetArray("Strain_CAR"),
out_vecs=[ref_mesh.GetCellData().GetArray("eR"),
ref_mesh.GetCellData().GetArray("eC"),
ref_mesh.GetCellData().GetArray("eL")],
verbose=0)
farray_strain_cyl.SetName("Strain_CYL")
mesh.GetCellData().AddArray(farray_strain_cyl)
if (ref_mesh is not None) and (ref_mesh.GetCellData().HasArray("eRR")) and (ref_mesh.GetCellData().HasArray("eCC")) and (ref_mesh.GetCellData().HasArray("eLL")):
farray_strain_pps = myVTK.rotateMatrix(
old_array=mesh.GetCellData().GetArray("Strain_CAR"),
out_vecs=[ref_mesh.GetCellData().GetArray("eRR"),
ref_mesh.GetCellData().GetArray("eCC"),
ref_mesh.GetCellData().GetArray("eLL")],
verbose=0)
farray_strain_pps.SetName("Strain_PPS")
mesh.GetCellData().AddArray(farray_strain_pps)
def getthresh(args):
inputfile = args[0]
outputfile = args[1]
sx = args[2]
ex = args[3]
sy = args[4]
ey = args[5]
sz = args[6]
ez = args[7]
dataset = args[8]
comptype = args[9]
print ("Loading file, %s" % inputfile)
#Determine if file is h5 or numpy
if (inputfile.split(".")[1] == "npy"):
rs = timeit.default_timer()
vel = np.load(inputfile)
re = timeit.default_timer()
else:
#read in file
rs = timeit.default_timer()
data_file = h5py.File(inputfile, 'r')
vel = np.array(data_file[dataset])
data_file.close()
re = timeit.default_timer()
cs = timeit.default_timer()
#convert numpy array to vtk
vtkdata = numpy_support.numpy_to_vtk(vel.flat, deep=True, array_type=vtk.VTK_FLOAT)
vtkdata.SetNumberOfComponents(3)
vtkdata.SetName("Velocity")
image = vtk.vtkImageData()
image.GetPointData().SetVectors(vtkdata)
image.SetExtent(sx,ex,sy,ey,sz,ez)
#NOTE: Hardcoding Spacing
image.SetSpacing(.006135923, .006135923, .006135923)
print ("Doing computation")
ce = timeit.default_timer()
vs = timeit.default_timer()
if (comptype == "v"):
vorticity = vtk.vtkCellDerivatives()
vorticity.SetVectorModeToComputeVorticity()
vorticity.SetTensorModeToPassTensors()
vorticity.SetInputData(image)
vorticity.Update()
elif (comptype == "q"):
vorticity = vtk.vtkGradientFilter()
vorticity.SetInputData(image)
vorticity.SetInputScalars(image.FIELD_ASSOCIATION_POINTS,"Velocity")
vorticity.ComputeQCriterionOn()
vorticity.SetComputeGradient(0)
vorticity.Update()
ve = timeit.default_timer()
#Generate contour for comparison
c = vtk.vtkContourFilter()
c.SetValue(0,1128)
if (comptype == "q"):
image.GetPointData().SetScalars(vorticity.GetOutput().GetPointData().GetVectors("Q-criterion"))
else:
image.GetPointData().SetScalars(vorticity.GetOutput().GetPointData().GetVectors())
c.SetInputData(image)
c.Update()
w = vtk.vtkXMLPolyDataWriter()
w.SetEncodeAppendedData(0) #turn of base 64 encoding for fast write
w.SetFileName("contour.vtp")
w.SetInputData(c.GetOutput())
ws = timeit.default_timer()
w.Write()
ms = timeit.default_timer()
if (comptype == "v"):
mag = vtk.vtkImageMagnitude()
cp = vtk.vtkCellDataToPointData()
cp.SetInputData(vorticity.GetOutput())
cp.Update()
image.GetPointData().SetScalars(cp.GetOutput().GetPointData().GetVectors())
mag.SetInputData(image)
mag.Update()
m = mag.GetOutput()
m.GetPointData().RemoveArray("Velocity")
else:
image.GetPointData().SetScalars(vorticity.GetOutput().GetPointData().GetVectors("Q-criterion"))
me = timeit.default_timer()
print ("Thresholding.")
ts = timeit.default_timer()
t = vtk.vtkImageThreshold()
#t = vtk.vtkThreshold() #sparse representation
if (comptype == "q"):
t.SetInputData(image)
t.ThresholdByUpper(783.3) #.25*67.17^2 = 1127
#t.SetInputArrayToProcess(0,0,0, vorticity.GetOutput().FIELD_ASSOCIATION_POINTS, "Q-criterion")
print("q criterion")
else:
t.SetInputData(m)
t.SetInputArrayToProcess(0,0,0, mag.GetOutput().FIELD_ASSOCIATION_POINTS, "Magnitude")
t.ThresholdByUpper(44.79) #44.79)
#Set values in range to 1 and values out of range to 0
t.SetInValue(1)
t.SetOutValue(0)
#t.ReplaceInOn()
#t.ReplaceOutOn()
print("Update thresh")
t.Update()
#wt = vtk.vtkXMLImageDataWriter()
#wt.SetInputData(t.GetOutput())
#wt.SetFileName("thresh.vti")
#wt.Write()
d = vtk.vtkImageDilateErode3D()
d.SetInputData(t.GetOutput())
d.SetKernelSize(3,3,3)
d.SetDilateValue(1)
d.SetErodeValue(0)
print ("Update dilate")
d.Update()
iis = vtk.vtkImageToImageStencil()
iis.SetInputData(d.GetOutput())
iis.ThresholdByUpper(1)
stencil = vtk.vtkImageStencil()
stencil.SetInputConnection(2, iis.GetOutputPort())
stencil.SetBackgroundValue(0)
#image.GetPointData().RemoveArray("Vorticity")
#Set scalars to velocity so it can be cut by the stencil
image.GetPointData().SetScalars(image.GetPointData().GetVectors())
#if (comptype == "q"): #Use this to get just q-criterion data instead of velocity data. Do we need both?
# image.GetPointData().SetScalars(vorticity.GetOutput().GetPointData().GetScalars("Q-criterion"))
stencil.SetInputData(image)
print ("Update stencil")
stencil.Update()
te = timeit.default_timer()
print("Setting up write")
ws = timeit.default_timer()
#Make velocity a vector again
velarray = stencil.GetOutput().GetPointData().GetScalars()
image.GetPointData().RemoveArray("Velocity")
image.GetPointData().SetVectors(velarray)
w = vtk.vtkXMLImageDataWriter()
w.SetCompressorTypeToZLib()
#w.SetCompressorTypeToNone() Need to figure out why this fails.
w.SetEncodeAppendedData(0) #turn of base 64 encoding for fast write
w.SetFileName(outputfile)
w.SetInputData(image)
if (0):
w.SetCompressorTypeToZfp()
w.GetCompressor().SetNx(ex-sx+1)
w.GetCompressor().SetNy(ey-sy+1)
w.GetCompressor().SetNz(ez-sz+1)
w.GetCompressor().SetTolerance(1e-1)
w.GetCompressor().SetNumComponents(3)
w.Write()
we = timeit.default_timer()
print("Results:")
print("Read time: %s" % str(re-rs))
print ("Convert to vtk: %s" % str(ce-cs))
if (comptype == "q"):
print ("Q Computation: %s" % str(ve-vs))
print ("Q Magnitude: %s" % str(me-ms))
else:
print ("Vorticity Computation: %s" % str(ve-vs))
print ("Vorticity Magnitude: %s" % str(me-ms))
print ("Threshold: %s" % str(te-ts))
print ("Write %s" % str(we-ws))
print ("Total time: %s" % str(we-rs))
def vortmesh(args):
p = args[0]
cubenum = args[1]
print("Cube", cubenum)
#Check for additonal parameters
if (p["param1"] != ''):
comptype = p["param1"]
else:
comptype = "q" #Default to q criterion
if (p["param2"] != ''):
thresh = float(p["param2"])
else:
thresh = 783.3 #Default for q threshold on isotropic data
inputfile = p["inputfile"] +str(cubenum) + ".npy" #Used so we can set either npy input or h5 input
outputfile = p["outputfile"] + str(cubenum) + ".vtp" #always VTK Image Data for this.
sx = p["sx"]
sy = p["sy"]
sz = p["sz"]
ex = p["ex"]
ey = p["ey"]
ez = p["ez"]
print ("Loading file, %s" % inputfile)
#Determine if file is h5 or numpy
rs = timeit.default_timer()
#In case file isn't here, catch this.
try:
vel = np.load(inputfile)
except:
p["message"] = "Failed to find file"
return p
re = timeit.default_timer()
#convert numpy array to vtk
cs = timeit.default_timer()
#convert numpy array to vtk
vtkdata = numpy_support.numpy_to_vtk(vel.flat, deep=True, array_type=vtk.VTK_FLOAT)
vtkdata.SetNumberOfComponents(3)
vtkdata.SetName("Velocity")
image = vtk.vtkImageData()
image.GetPointData().SetVectors(vtkdata)
image.SetExtent(sx,ex,sy,ey,sz,ez)
#NOTE: Hardcoding Spacing TODO: Add to parameters
image.SetSpacing(.006135923, .006135923, .006135923)
ce = timeit.default_timer()
vs = timeit.default_timer()
if (comptype == "v"):
vorticity = vtk.vtkCellDerivatives()
vorticity.SetVectorModeToComputeVorticity()
vorticity.SetTensorModeToPassTensors()
vorticity.SetInputData(image)
vorticity.Update()
elif (comptype == "q"):
vorticity = vtk.vtkGradientFilter()
vorticity.SetInputData(image)
vorticity.SetInputScalars(image.FIELD_ASSOCIATION_POINTS,"Velocity")
vorticity.ComputeQCriterionOn()
vorticity.SetComputeGradient(0)
vorticity.Update()
ve = timeit.default_timer()
#Generate contour for comparison
c = vtk.vtkContourFilter()
c.SetValue(0,thresh)
if (comptype == "q"):
image.GetPointData().SetScalars(vorticity.GetOutput().GetPointData().GetVectors("Q-criterion"))
else:
image.GetPointData().SetScalars(vorticity.GetOutput().GetPointData().GetVectors())
c.SetInputData(image)
c.Update()
w = vtk.vtkXMLPolyDataWriter()
w.SetEncodeAppendedData(0) #turn of base 64 encoding for fast write
w.SetFileName(outputfile)
w.SetInputData(c.GetOutput())
ws = timeit.default_timer()
result = w.Write()
we = timeit.default_timer()
print("Read time: %s" % str(re-rs))
print ("Convert to vtk: %s" % str(ce-cs))
if (comptype == "q"):
print ("Q Computation: %s" % str(ve-vs))
else:
print ("Vorticity Computation: %s" % str(ve-vs))
print ("Write %s" % str(we-ws))
print ("Total time: %s" % str(we-rs))
if (result):
p["message"] = "Success"
p["computetime"] = str(we-rs)
return p #return the packet
def vortvelvolume(args):
#inputfile, outputfile, sx, ex, sy, ey, sz, ez, dataset):
p = args[0]
cubenum = args[1]
print("Cube", cubenum)
#Check for additonal parameters
if (p["param1"] != ''):
comptype = p["param1"]
else:
comptype = "q" #Default to q criterion
if (p["param2"] != ''):
thresh = float(p["param2"])
else:
thresh = 783.3 #Default for q threshold on isotropic data
#We use 0 for structured grid (vti) and 1 for unstructured grid (vtu)
if (p["param3"] != ''):
grid = 0
else:
grid = 1
if (p["param4"] != ''):
kernelsize = int(p["param4"])
else:
kernelsize = 3
inputfile = p["inputfile"] +str(cubenum) + ".npy"
outputfile = p["outputfile"] + str(cubenum) + ".vti" #always VTK Image Data for this.
sx = p["sx"]
sy = p["sy"]
sz = p["sz"]
ex = p["ex"]
ey = p["ey"]
ez = p["ez"]
print ("Loading file, %s" % inputfile)
#Determine if file is h5 or numpy
rs = timeit.default_timer()
vel = np.load(inputfile)
re = timeit.default_timer()
#convert numpy array to vtk
cs = timeit.default_timer()
#convert numpy array to vtk
vtkdata = numpy_support.numpy_to_vtk(vel.flat, deep=True, array_type=vtk.VTK_FLOAT)
vtkdata.SetNumberOfComponents(3)
vtkdata.SetName("Velocity")
image = vtk.vtkImageData()
image.GetPointData().SetVectors(vtkdata)
image.SetExtent(sx,ex,sy,ey,sz,ez)
#NOTE: Hardcoding Spacing
image.SetSpacing(.006135923, .006135923, .006135923)
ce = timeit.default_timer()
vs = timeit.default_timer()
if (comptype == "v"):
vorticity = vtk.vtkCellDerivatives()
vorticity.SetVectorModeToComputeVorticity()
vorticity.SetTensorModeToPassTensors()
vorticity.SetInputData(image)
vorticity.Update()
elif (comptype == "q"):
vorticity = vtk.vtkGradientFilter()
vorticity.SetInputData(image)
vorticity.SetInputScalars(image.FIELD_ASSOCIATION_POINTS,"Velocity")
vorticity.ComputeQCriterionOn()
vorticity.SetComputeGradient(0)
vorticity.Update()
ve = timeit.default_timer()
ms = timeit.default_timer()
if (comptype == "v"):
mag = vtk.vtkImageMagnitude()
cp = vtk.vtkCellDataToPointData()
cp.SetInputData(vorticity.GetOutput())
cp.Update()
image.GetPointData().SetScalars(cp.GetOutput().GetPointData().GetVectors())
mag.SetInputData(image)
mag.Update()
m = mag.GetOutput()
m.GetPointData().RemoveArray("Velocity")
else:
image.GetPointData().SetScalars(vorticity.GetOutput().GetPointData().GetVectors("Q-criterion"))
me = timeit.default_timer()
print ("Thresholding.")
ts = timeit.default_timer()
t = vtk.vtkImageThreshold()
#t = vtk.vtkThreshold() #sparse representation
if (comptype == "q"):
t.SetInputData(image)
t.ThresholdByUpper(thresh) #.25*67.17^2 = 1127
#t.SetInputArrayToProcess(0,0,0, vorticity.GetOutput().FIELD_ASSOCIATION_POINTS, "Q-criterion")
print("q criterion")
else:
t.SetInputData(m)
t.SetInputArrayToProcess(0,0,0, mag.GetOutput().FIELD_ASSOCIATION_POINTS, "Magnitude")
t.ThresholdByUpper(thresh) #44.79)
#Set values in range to 1 and values out of range to 0
t.SetInValue(1)
t.SetOutValue(0)
#t.ReplaceInOn()
#t.ReplaceOutOn()
print("Update thresh")
t.Update()
#wt = vtk.vtkXMLImageDataWriter()
#wt.SetInputData(t.GetOutput())
#wt.SetFileName("thresh.vti")
#wt.Write()
d = vtk.vtkImageDilateErode3D()
d.SetInputData(t.GetOutput())
d.SetKernelSize(kernelsize,kernelsize,kernelsize)
d.SetDilateValue(1)
d.SetErodeValue(0)
print ("Update dilate")
d.Update()
iis = vtk.vtkImageToImageStencil()
iis.SetInputData(d.GetOutput())
iis.ThresholdByUpper(1)
stencil = vtk.vtkImageStencil()
stencil.SetInputConnection(2, iis.GetOutputPort())
stencil.SetBackgroundValue(0)
#image.GetPointData().RemoveArray("Vorticity")
#Set scalars to velocity so it can be cut by the stencil
image.GetPointData().SetScalars(image.GetPointData().GetVectors())
#if (comptype == "q"): #Use this to get just q-criterion data instead of velocity data. Do we need both?
# image.GetPointData().SetScalars(vorticity.GetOutput().GetPointData().GetScalars("Q-criterion"))
stencil.SetInputData(image)
print ("Update stencil")
stencil.Update()
te = timeit.default_timer()
print("Setting up write")
ws = timeit.default_timer()
#Make velocity a vector again
velarray = stencil.GetOutput().GetPointData().GetScalars()
image.GetPointData().RemoveArray("Velocity")
image.GetPointData().SetVectors(velarray)
if (grid == 0):
w = vtk.vtkXMLImageDataWriter()
else:
w = vtk.vtkXMLUnstructuredGridWriter()
w.SetCompressorTypeToZLib()
#w.SetCompressorTypeToNone() Need to figure out why this fails.
w.SetEncodeAppendedData(0) #turn of base 64 encoding for fast write
w.SetFileName(outputfile)
w.SetInputData(image)
if (0):
w.SetCompressorTypeToZfp()
w.GetCompressor().SetNx(ex-sx+1)
w.GetCompressor().SetNy(ey-sy+1)
w.GetCompressor().SetNz(ez-sz+1)
w.GetCompressor().SetTolerance(1e-2)
w.GetCompressor().SetNumComponents(3)
result = w.Write()
result = 1 #don't write for benchmarking
we = timeit.default_timer()
print("Results:")
print("Read time: %s" % str(re-rs))
print ("Convert to vtk: %s" % str(ce-cs))
if (comptype == "q"):
print ("Q Computation: %s" % str(ve-vs))
print ("Q Magnitude: %s" % str(me-ms))
else:
print ("Vorticity Computation: %s" % str(ve-vs))
print ("Vorticity Magnitude: %s" % str(me-ms))
print ("Threshold: %s" % str(te-ts))
print ("Write %s" % str(we-ws))
print ("Total time: %s" % str(we-rs))
if (result):
p["message"] = "Success"
p["computetime"] = str(we-rs)
return p #return the packet
def vortvelvolumei(args):
#inputfile, outputfile, sx, ex, sy, ey, sz, ez, dataset):
p = args[0]
cubenum = args[1]
print("Cube", cubenum)
#Check for additonal parameters
if (p["param1"] != ''):
comptype = p["param1"]
else:
comptype = "q" #Default to q criterion
if (p["param2"] != ''):
thresh = float(p["param2"])
else:
thresh = 783.3 #Default for q threshold on isotropic data
inputfile = p["inputfile"] +str(cubenum) + ".npy"
outputfile = p["outputfile"] + str(cubenum) + ".vti" #always VTK Image Data for this.
sx = p["sx"]
sy = p["sy"]
sz = p["sz"]
ex = p["ex"]
ey = p["ey"]
ez = p["ez"]
print ("Loading file, %s" % inputfile)
#Determine if file is h5 or numpy
rs = timeit.default_timer()
vel = np.load(inputfile)
print ("File Loaded")
re = timeit.default_timer()
#convert numpy array to vtk
cs = timeit.default_timer()
#convert numpy array to vtk
vtkdata = numpy_support.numpy_to_vtk(vel.flat, deep=True, array_type=vtk.VTK_FLOAT)
vtkdata.SetNumberOfComponents(3)
vtkdata.SetName("Velocity")
image = vtk.vtkImageData()
image.GetPointData().SetVectors(vtkdata)
image.SetExtent(sx,ex,sy,ey,sz,ez)
#NOTE: Hardcoding Spacing
image.SetSpacing(.006135923, .006135923, .006135923)
ce = timeit.default_timer()
vs = timeit.default_timer()
print ("Beginning computation: " + comptype)
if (comptype == "v"):
vorticity = vtk.vtkCellDerivatives()
vorticity.SetVectorModeToComputeVorticity()
vorticity.SetTensorModeToPassTensors()
vorticity.SetInputData(image)
vorticity.Update()
elif (comptype == "q"):
vorticity = vtk.vtkGradientFilter()
vorticity.SetInputData(image)
vorticity.SetInputScalars(image.FIELD_ASSOCIATION_POINTS,"Velocity")
vorticity.ComputeQCriterionOn()
vorticity.SetComputeGradient(0)
vorticity.Update()
ve = timeit.default_timer()
print("Initial calculation done")
ms = timeit.default_timer()
if (comptype == "v"):
mag = vtk.vtkImageMagnitude()
cp = vtk.vtkCellDataToPointData()
cp.SetInputData(vorticity.GetOutput())
cp.Update()
image.GetPointData().SetScalars(cp.GetOutput().GetPointData().GetVectors())
mag.SetInputData(image)
mag.Update()
m = mag.GetOutput()
m.GetPointData().RemoveArray("Velocity")
else:
image.GetPointData().SetScalars(vorticity.GetOutput().GetPointData().GetVectors("Q-criterion"))
me = timeit.default_timer()
print("Generating screenshot")
c = vtk.vtkContourFilter()
c.SetValue(0,thresh)
c.SetInputData(image)
c.Update()
contour = c.GetOutput()
mapper = vtk.vtkPolyDataMapper()
mapper.SetInputData(contour)
mapper.ScalarVisibilityOn()
mapper.SetScalarRange(-1,1)
mapper.SetScalarModeToUsePointFieldData()
mapper.ColorByArrayComponent("Velocity", 0)
actor = vtk.vtkActor()
actor.SetMapper(mapper)
ren = vtk.vtkRenderer()
ren.AddActor(actor)
ren.SetBackground(1,1,1)
camera = vtk.vtkCamera()
ren.SetActiveCamera(camera)
ren.ResetCamera()
camera.Zoom(1.5) #This reduces the whitespace around the image
renWin = vtk.vtkRenderWindow()
renWin.SetSize(1024,1024)
renWin.AddRenderer(ren)
renWin.SetOffScreenRendering(1)
windowToImageFilter = vtk.vtkWindowToImageFilter()
windowToImageFilter.SetInput(renWin)
windowToImageFilter.Update()
w = vtk.vtkPNGWriter()
pngfilename = p["outputfile"] + str(cubenum) + ".png"
w.SetFileName(pngfilename)
w.SetInputConnection(windowToImageFilter.GetOutputPort())
w.Write()
#Shift camera angle and take snapshots around the cube.
for aznum in range(4):
camera.Azimuth(90)
windowToImageFilter = vtk.vtkWindowToImageFilter()
windowToImageFilter.SetInput(renWin)
windowToImageFilter.Update()
pngfilename = p["outputfile"] + str(cubenum) + "-r" + str(aznum)+ ".png"
w.SetFileName(pngfilename)
w.SetInputConnection(windowToImageFilter.GetOutputPort())
w.Write()
camera.Elevation(90) #Rotate camera to top
windowToImageFilter = vtk.vtkWindowToImageFilter()
windowToImageFilter.SetInput(renWin)
windowToImageFilter.Update()
pngfilename = p["outputfile"] + str(cubenum) + "-t1.png"
w.SetFileName(pngfilename)
w.SetInputConnection(windowToImageFilter.GetOutputPort())
w.Write()
camera.Elevation(180) #Rotate camera to bottom
windowToImageFilter = vtk.vtkWindowToImageFilter()
windowToImageFilter.SetInput(renWin)
windowToImageFilter.Update()
pngfilename = p["outputfile"] + str(cubenum) + "-b1.png"
w.SetFileName(pngfilename)
w.SetInputConnection(windowToImageFilter.GetOutputPort())
w.Write()
print ("Thresholding.")
ts = timeit.default_timer()
t = vtk.vtkImageThreshold() #Dense represenation (0's included, structured grid)
#t = vtk.vtkThreshold() #sparse representation
if (comptype == "q"):
t.SetInputData(image)
t.ThresholdByUpper(thresh) #.25*67.17^2 = 1127
#t.SetInputArrayToProcess(0,0,0, vorticity.GetOutput().FIELD_ASSOCIATION_POINTS, "Q-criterion")
print("q criterion")
else:
t.SetInputData(m)
t.SetInputArrayToProcess(0,0,0, mag.GetOutput().FIELD_ASSOCIATION_POINTS, "Magnitude")
t.ThresholdByUpper(thresh) #44.79)
#Set values in range to 1 and values out of range to 0
t.SetInValue(1)
t.SetOutValue(0)
#t.ReplaceInOn()
#t.ReplaceOutOn()
print("Update thresh")
t.Update()
#wt = vtk.vtkXMLImageDataWriter()
#wt.SetInputData(t.GetOutput())
#wt.SetFileName("thresh.vti")
#wt.Write()
d = vtk.vtkImageDilateErode3D()
d.SetInputData(t.GetOutput())
d.SetKernelSize(4,4,4)
d.SetDilateValue(1)
d.SetErodeValue(0)
print ("Update dilate")
d.Update()
iis = vtk.vtkImageToImageStencil()
iis.SetInputData(d.GetOutput())
iis.ThresholdByUpper(1)
stencil = vtk.vtkImageStencil()
stencil.SetInputConnection(2, iis.GetOutputPort())
stencil.SetBackgroundValue(0)
#image.GetPointData().RemoveArray("Vorticity")
#Set scalars to velocity so it can be cut by the stencil
image.GetPointData().SetScalars(image.GetPointData().GetVectors())
#if (comptype == "q"): #Use this to get just q-criterion data instead of velocity data. Do we need both?
# image.GetPointData().SetScalars(vorticity.GetOutput().GetPointData().GetScalars("Q-criterion"))
stencil.SetInputData(image)
print ("Update stencil")
stencil.Update()
te = timeit.default_timer()
print("Setting up write")
ws = timeit.default_timer()
#Make velocity a vector again
velarray = stencil.GetOutput().GetPointData().GetScalars()
image.GetPointData().RemoveArray("Velocity")
image.GetPointData().SetVectors(velarray)
w = vtk.vtkXMLImageDataWriter()
w.SetCompressorTypeToZLib()
#w.SetCompressorTypeToNone() Need to figure out why this fails.
w.SetEncodeAppendedData(0) #turn of base 64 encoding for fast write
w.SetFileName(outputfile)
w.SetInputData(image)
if (0):
w.SetCompressorTypeToZfp()
w.GetCompressor().SetNx(ex-sx+1)
w.GetCompressor().SetNy(ey-sy+1)
w.GetCompressor().SetNz(ez-sz+1)
w.GetCompressor().SetTolerance(1e-2)
w.GetCompressor().SetNumComponents(3)
#result = w.Write()
result = 1 #don't write for benchmarking
we = timeit.default_timer()
print("Results:")
print("Read time: %s" % str(re-rs))
print ("Convert to vtk: %s" % str(ce-cs))
if (comptype == "q"):
print ("Q Computation: %s" % str(ve-vs))
print ("Q Magnitude: %s" % str(me-ms))
else:
print ("Vorticity Computation: %s" % str(ve-vs))
print ("Vorticity Magnitude: %s" % str(me-ms))
print ("Threshold: %s" % str(te-ts))
print ("Write %s" % str(we-ws))
print ("Total time: %s" % str(we-rs))
if (result):
p["message"] = "Success"
p["computetime"] = str(we-rs)
return p #return the packet
print("GU = " + str(GU))
for k_point in range(8):
farray_disp.SetTuple(k_point, numpy.dot(GU, points.GetPoint(k_point)))
#print farray_disp.GetTuple(k_point)
# Compute the small (linearized) strain tensor: e = (GU)_sym = (GU+GU^T)/2
e = (GU + numpy.transpose(GU)) / 2
print("e = " + str(e))
# Compute the Green-Lagrange strain tensor: E = (F.F^T-1)/2 = (GU+GU^T+GU^T.GU)/2 = e + GU^T.GU/2
E = e + numpy.dot(numpy.transpose(GU), GU) / 2
print("E = " + str(E))
# Compute displacement gradient using vtkCellDerivatives
cell_derivatives = vtk.vtkCellDerivatives()
cell_derivatives.SetVectorModeToPassVectors()
cell_derivatives.SetTensorModeToComputeGradient()
cell_derivatives.SetInputData(ugrid_hex)
cell_derivatives.Update()
vector_gradient = numpy.reshape(
cell_derivatives.GetOutput().GetCellData().GetArray(
"VectorGradient").GetTuple(0), (3, 3))
print("VectorGradient = " + str(vector_gradient))
assert numpy.allclose(vector_gradient, GU)
# Compute small strain tensor using vtkCellDerivatives
cell_derivatives = vtk.vtkCellDerivatives()
cell_derivatives.SetVectorModeToPassVectors()
cell_derivatives.SetTensorModeToComputeStrain()
cell_derivatives.SetInputData(ugrid_hex)
def computeStrainsFromDisplacements(mesh,
disp_array_name="displacement",
ref_mesh=None,
verbose=0):
myVTK.myPrint(verbose, "*** computeStrainsFromDisplacements ***")
myVTK.myPrint(
min(verbose, 1),
"*** Warning: at some point the ordering of vector gradient components has changed, and uses C ordering instead of F. ***"
)
if (vtk.vtkVersion.GetVTKMajorVersion() >= 8):
ordering = "C"
elif (vtk.vtkVersion.GetVTKMajorVersion()
== 7) and ((vtk.vtkVersion.GetVTKMinorVersion() > 0) or
(vtk.vtkVersion.GetVTKBuildVersion() > 0)):
ordering = "C"
else:
ordering = "F"
n_points = mesh.GetNumberOfPoints()
n_cells = mesh.GetNumberOfCells()
assert (mesh.GetPointData().HasArray(disp_array_name))
mesh.GetPointData().SetActiveVectors(disp_array_name)
cell_derivatives = vtk.vtkCellDerivatives()
cell_derivatives.SetVectorModeToPassVectors()
cell_derivatives.SetTensorModeToComputeGradient()
if (vtk.vtkVersion.GetVTKMajorVersion() >= 6):
cell_derivatives.SetInputData(mesh)
else:
cell_derivatives.SetInput(mesh)
cell_derivatives.Update()
farray_gu = cell_derivatives.GetOutput().GetCellData().GetArray(
"VectorGradient")
if (ref_mesh is not None):
farray_strain = myVTK.createFloatArray(name="Strain_CAR",
n_components=6,
n_tuples=n_cells)
else:
farray_strain = myVTK.createFloatArray(name="Strain",
n_components=6,
n_tuples=n_cells)
mesh.GetCellData().AddArray(farray_strain)
I = numpy.eye(3)
E_vec = numpy.empty(6)
#e_vec = numpy.empty(6)
for k_cell in range(n_cells):
GU = numpy.reshape(farray_gu.GetTuple(k_cell), (3, 3), ordering)
F = I + GU
C = numpy.dot(numpy.transpose(F), F)
E = (C - I) / 2
mat_sym33_to_vec_col6(E, E_vec)
farray_strain.SetTuple(k_cell, E_vec)
#if (add_almansi_strain):
#Finv = numpy.linalg.inv(F)
#c = numpy.dot(numpy.transpose(Finv), Finv)
#e = (I - c)/2
#mat_sym33_to_vec_col6(e, e_vec)
#farray_almansi.SetTuple(k_cell, e_vec)
if (ref_mesh is not None) and (ref_mesh.GetCellData().HasArray("eR")) and (
ref_mesh.GetCellData().HasArray("eC")) and (
ref_mesh.GetCellData().HasArray("eL")):
farray_strain_cyl = myVTK.rotateMatrix(
old_array=mesh.GetCellData().GetArray("Strain_CAR"),
out_vecs=[
ref_mesh.GetCellData().GetArray("eR"),
ref_mesh.GetCellData().GetArray("eC"),
ref_mesh.GetCellData().GetArray("eL")
],
verbose=0)
farray_strain_cyl.SetName("Strain_CYL")
mesh.GetCellData().AddArray(farray_strain_cyl)
if (ref_mesh
is not None) and (ref_mesh.GetCellData().HasArray("eRR")) and (
ref_mesh.GetCellData().HasArray("eCC")) and (
ref_mesh.GetCellData().HasArray("eLL")):
farray_strain_pps = myVTK.rotateMatrix(
old_array=mesh.GetCellData().GetArray("Strain_CAR"),
out_vecs=[
ref_mesh.GetCellData().GetArray("eRR"),
ref_mesh.GetCellData().GetArray("eCC"),
ref_mesh.GetCellData().GetArray("eLL")
],
verbose=0)
farray_strain_pps.SetName("Strain_PPS")
mesh.GetCellData().AddArray(farray_strain_pps)
def getthresh(args):
inputfile = args[0]
outputfile = args[1]
sx = args[2]
ex = args[3]
sy = args[4]
ey = args[5]
sz = args[6]
ez = args[7]
dataset = args[8]
comptype = args[9]
print("Loading file, %s" % inputfile)
#Determine if file is h5 or numpy
if (inputfile.split(".")[1] == "npy"):
rs = timeit.default_timer()
vel = np.load(inputfile)
re = timeit.default_timer()
else:
#read in file
rs = timeit.default_timer()
data_file = h5py.File(inputfile, 'r')
vel = np.array(data_file[dataset])
data_file.close()
re = timeit.default_timer()
cs = timeit.default_timer()
#convert numpy array to vtk
vtkdata = numpy_support.numpy_to_vtk(vel.flat,
deep=True,
array_type=vtk.VTK_FLOAT)
vtkdata.SetNumberOfComponents(3)
vtkdata.SetName("Velocity")
image = vtk.vtkImageData()
image.GetPointData().SetVectors(vtkdata)
image.SetExtent(sx, ex, sy, ey, sz, ez)
#NOTE: Hardcoding Spacing
image.SetSpacing(.006135923, .006135923, .006135923)
print("Doing computation")
ce = timeit.default_timer()
vs = timeit.default_timer()
if (comptype == "v"):
vorticity = vtk.vtkCellDerivatives()
vorticity.SetVectorModeToComputeVorticity()
vorticity.SetTensorModeToPassTensors()
vorticity.SetInputData(image)
vorticity.Update()
elif (comptype == "q"):
vorticity = vtk.vtkGradientFilter()
vorticity.SetInputData(image)
vorticity.SetInputScalars(image.FIELD_ASSOCIATION_POINTS, "Velocity")
vorticity.ComputeQCriterionOn()
vorticity.SetComputeGradient(0)
vorticity.Update()
ve = timeit.default_timer()
#Generate contour for comparison
c = vtk.vtkContourFilter()
c.SetValue(0, 1128)
if (comptype == "q"):
image.GetPointData().SetScalars(
vorticity.GetOutput().GetPointData().GetVectors("Q-criterion"))
else:
image.GetPointData().SetScalars(
vorticity.GetOutput().GetPointData().GetVectors())
c.SetInputData(image)
c.Update()
w = vtk.vtkXMLPolyDataWriter()
w.SetEncodeAppendedData(0) #turn of base 64 encoding for fast write
w.SetFileName("contour.vtp")
w.SetInputData(c.GetOutput())
ws = timeit.default_timer()
w.Write()
ms = timeit.default_timer()
if (comptype == "v"):
mag = vtk.vtkImageMagnitude()
cp = vtk.vtkCellDataToPointData()
cp.SetInputData(vorticity.GetOutput())
cp.Update()
image.GetPointData().SetScalars(
cp.GetOutput().GetPointData().GetVectors())
mag.SetInputData(image)
mag.Update()
m = mag.GetOutput()
m.GetPointData().RemoveArray("Velocity")
else:
image.GetPointData().SetScalars(
vorticity.GetOutput().GetPointData().GetVectors("Q-criterion"))
me = timeit.default_timer()
print("Thresholding.")
ts = timeit.default_timer()
t = vtk.vtkImageThreshold()
#t = vtk.vtkThreshold() #sparse representation
if (comptype == "q"):
t.SetInputData(image)
t.ThresholdByUpper(783.3) #.25*67.17^2 = 1127
#t.SetInputArrayToProcess(0,0,0, vorticity.GetOutput().FIELD_ASSOCIATION_POINTS, "Q-criterion")
print("q criterion")
else:
t.SetInputData(m)
t.SetInputArrayToProcess(0, 0, 0,
mag.GetOutput().FIELD_ASSOCIATION_POINTS,
"Magnitude")
t.ThresholdByUpper(44.79) #44.79)
#Set values in range to 1 and values out of range to 0
t.SetInValue(1)
t.SetOutValue(0)
#t.ReplaceInOn()
#t.ReplaceOutOn()
print("Update thresh")
t.Update()
#wt = vtk.vtkXMLImageDataWriter()
#wt.SetInputData(t.GetOutput())
#wt.SetFileName("thresh.vti")
#wt.Write()
d = vtk.vtkImageDilateErode3D()
d.SetInputData(t.GetOutput())
d.SetKernelSize(3, 3, 3)
d.SetDilateValue(1)
d.SetErodeValue(0)
print("Update dilate")
d.Update()
iis = vtk.vtkImageToImageStencil()
iis.SetInputData(d.GetOutput())
iis.ThresholdByUpper(1)
stencil = vtk.vtkImageStencil()
stencil.SetInputConnection(2, iis.GetOutputPort())
stencil.SetBackgroundValue(0)
#image.GetPointData().RemoveArray("Vorticity")
#Set scalars to velocity so it can be cut by the stencil
image.GetPointData().SetScalars(image.GetPointData().GetVectors())
#if (comptype == "q"): #Use this to get just q-criterion data instead of velocity data. Do we need both?
# image.GetPointData().SetScalars(vorticity.GetOutput().GetPointData().GetScalars("Q-criterion"))
stencil.SetInputData(image)
print("Update stencil")
stencil.Update()
te = timeit.default_timer()
print("Setting up write")
ws = timeit.default_timer()
#Make velocity a vector again
velarray = stencil.GetOutput().GetPointData().GetScalars()
image.GetPointData().RemoveArray("Velocity")
image.GetPointData().SetVectors(velarray)
w = vtk.vtkXMLImageDataWriter()
w.SetCompressorTypeToZLib()
#w.SetCompressorTypeToNone() Need to figure out why this fails.
w.SetEncodeAppendedData(0) #turn of base 64 encoding for fast write
w.SetFileName(outputfile)
w.SetInputData(image)
if (0):
w.SetCompressorTypeToZfp()
w.GetCompressor().SetNx(ex - sx + 1)
w.GetCompressor().SetNy(ey - sy + 1)
w.GetCompressor().SetNz(ez - sz + 1)
w.GetCompressor().SetTolerance(1e-1)
w.GetCompressor().SetNumComponents(3)
w.Write()
we = timeit.default_timer()
print("Results:")
print("Read time: %s" % str(re - rs))
print("Convert to vtk: %s" % str(ce - cs))
if (comptype == "q"):
print("Q Computation: %s" % str(ve - vs))
print("Q Magnitude: %s" % str(me - ms))
else:
print("Vorticity Computation: %s" % str(ve - vs))
print("Vorticity Magnitude: %s" % str(me - ms))
print("Threshold: %s" % str(te - ts))
print("Write %s" % str(we - ws))
print("Total time: %s" % str(we - rs))
def main(argv):
try:
opts, args = getopt.getopt(argv, "hi:o:x:a:y:b:z:c:d:u:", [
"ifile=", "ofile=", "sx=", "ex=", "sy=", "ez=", "dataset=", "comp="
])
except getopt.GetoptError as err:
print 'getmultithresh.py -i <inputfile.h5> -o <outputfile.vti> -sx -ex -sy -ey -sz -ez -dataset -comptype'
print(str(err))
for opt, arg in opts:
if opt == '-h':
print 'getmultithresh.py -i <inputfile.h5> -o <outputfile.vti> -sx -ex -sy -ey -sz -ez -dataset'
sys.exit()
elif opt in ("-i", "--ifile"):
inputfile = arg
elif opt in ("-o", "--ofile"):
outputfile = arg
elif opt in ("-x", "--sx"):
sx = int(arg)
elif opt in ("-a", "--ex"):
ex = int(arg)
elif opt in ("-y", "--sy"):
sy = int(arg)
elif opt in ("-b", "--ey"):
ey = int(arg)
elif opt in ("-z", "--sz"):
sz = int(arg)
elif opt in ("-c", "--ez"):
ez = int(arg)
elif opt in ("-d", "--dataset"):
dataset = str(arg)
elif opt in ("-u", "--du"):
comptype = str(arg)
print("Loading file, %s" % inputfile)
#Determine if file is h5 or numpy
if (inputfile.split(".")[1] == "npy"):
rs = timeit.default_timer()
vel = np.load(inputfile)
re = timeit.default_timer()
else:
#read in file
rs = timeit.default_timer()
data_file = h5py.File(inputfile, 'r')
vel = np.array(data_file[dataset])
data_file.close()
re = timeit.default_timer()
cs = timeit.default_timer()
#convert numpy array to vtk
vtkdata = numpy_support.numpy_to_vtk(vel.flat,
deep=True,
array_type=vtk.VTK_FLOAT)
vtkdata.SetNumberOfComponents(3)
vtkdata.SetName("Velocity")
image = vtk.vtkImageData()
image.GetPointData().SetVectors(vtkdata)
image.SetExtent(sx, ex, sy, ey, sz, ez)
#NOTE: Hardcoding Spacing
image.SetSpacing(.006135923, .006135923, .006135923)
print("Doing computation")
ce = timeit.default_timer()
vs = timeit.default_timer()
ve = timeit.default_timer()
print("Generating contour")
ms = timeit.default_timer()
mag = vtk.vtkImageMagnitude()
for x in range(0, 1):
start = timeit.default_timer()
threshold = (22.39 * (2.5))
if (comptype == "q"):
threshold = (783.3)
vort = vtk.vtkGradientFilter()
vort.SetInputData(image)
vort.SetInputScalars(image.FIELD_ASSOCIATION_POINTS, "Velocity")
vort.ComputeQCriterionOn()
vort.Update()
image.GetPointData().SetScalars(
vort.GetOutput().GetPointData().GetVectors("Q-criterion"))
else:
v = vtk.vtkCellDerivatives()
v.SetVectorModeToComputeVorticity()
v.SetTensorModeToPassTensors()
v.SetInputData(image)
v.Update()
vort = vtk.vtkImageMagnitude()
cp = vtk.vtkCellDataToPointData()
cp.SetInputData(v.GetOutput())
cp.Update()
image.GetPointData().SetScalars(
cp.GetOutput().GetPointData().GetVectors())
vort.SetInputData(image)
vort.Update()
#ni = vtk.vtkImageData()
#ni.SetSpacing(.006135923, .006135923, .006135923)
#ni.SetExtent(sx,ex,sy,ey,sz,ez)
#ni.GetPointData().SetScalars(q.GetOutput().GetPointData().GetVectors("Q-criterion"))
mend = timeit.default_timer()
me = mend
comptime = mend - start
print("Magnitude Computation time: " + str(comptime) + "s")
c = vtk.vtkContourFilter()
c.SetValue(0, threshold)
if (comptype == "q"):
c.SetInputData(image)
else:
c.SetInputData(vort.GetOutput())
print("Computing Contour with threshold", threshold)
c.Update()
w = vtk.vtkXMLPolyDataWriter()
w.SetEncodeAppendedData(0) #turn of base 64 encoding for fast write
w.SetFileName(outputfile + str(x) + ".vtp ")
w.SetInputData(c.GetOutput())
ws = timeit.default_timer()
w.Write()
we = timeit.default_timer()
print("Results:")
print("Read time: %s" % str(re - rs))
print("Convert to vtk: %s" % str(ce - cs))
if (comptype == "q"):
print("Q Computation: %s" % str(ve - vs))
print("Q Magnitude: %s" % str(me - ms))
else:
print("Vorticity Computation: %s" % str(ve - vs))
print("Vorticity Magnitude: %s" % str(me - ms))
#print ("Threshold: %s" % str(te-ts))
print("Write %s" % str(we - ws))
print("Total time: %s" % str(we - rs))
print("GU = " + str(GU))
for k_point in xrange(8):
farray_disp.SetTuple(k_point, numpy.dot(GU, points.GetPoint(k_point)))
# print farray_disp.GetTuple(k_point)
# Compute the small (linearized) strain tensor: e = (GU)_sym = (GU+GU^T)/2
e = (GU + numpy.transpose(GU)) / 2
print("e = " + str(e))
# Compute the Green-Lagrange strain tensor: E = (F.F^T-1)/2 = (GU+GU^T+GU^T.GU)/2 = e + GU^T.GU/2
E = e + numpy.dot(numpy.transpose(GU), GU) / 2
print("E = " + str(E))
# Compute displacement gradient using vtkCellDerivatives
cell_derivatives = vtk.vtkCellDerivatives()
cell_derivatives.SetVectorModeToPassVectors()
cell_derivatives.SetTensorModeToComputeGradient()
cell_derivatives.SetInputData(ugrid_hex)
cell_derivatives.Update()
vector_gradient = numpy.reshape(
cell_derivatives.GetOutput().GetCellData().GetArray("VectorGradient").GetTuple(0), (3, 3)
)
print("VectorGradient = " + str(vector_gradient))
assert numpy.allclose(vector_gradient, GU)
# Compute small strain tensor using vtkCellDerivatives
cell_derivatives = vtk.vtkCellDerivatives()
cell_derivatives.SetVectorModeToPassVectors()
cell_derivatives.SetTensorModeToComputeStrain()
cell_derivatives.SetInputData(ugrid_hex)
def deformableRegistration(self):
"""
Performs deformable image registration on images reconstructed from polygonal surfaces at a user-specified precision.
If **animate** parameter is *True*, this also spawns a VTK interative rendering that can animate the deformation.
Returns
-------
cell_fields
"""
for r, mesh in enumerate(self.rmeshes):
print(("Performing deformable image registration for object {:d}".
format(r + 1)))
rimg, dimg, rpoly = self._poly2img(r)
origin = rimg.GetOrigin()
rimg.SetOrigin((0, 0, 0))
dimg.SetOrigin((0, 0, 0))
steplength = np.min(dimg.GetSpacing()) * 5.0
rimg = sitk.AntiAliasBinary(rimg)
dimg = sitk.AntiAliasBinary(dimg)
#peform the deformable registration
register = sitk.FastSymmetricForcesDemonsRegistrationFilter()
register.SetNumberOfIterations(
self.deformableSettings['Iterations'])
register.SetMaximumRMSError(self.deformableSettings['Maximum RMS'])
register.SmoothDisplacementFieldOn()
register.SetStandardDeviations(
self.deformableSettings['Displacement Smoothing'])
register.SmoothUpdateFieldOff()
register.UseImageSpacingOn()
register.SetMaximumUpdateStepLength(steplength)
register.SetUseGradientType(0)
disp_field = register.Execute(rimg, dimg)
print(("...Elapsed iterations: {:d}".format(
register.GetElapsedIterations())))
print(("...Change in RMS error: {:6.3f}".format(
register.GetRMSChange())))
disp_field.SetOrigin(origin)
#translate displacement field to VTK regular grid
a = sitk.GetArrayFromImage(disp_field)
disp = vtk.vtkImageData()
disp.SetOrigin(disp_field.GetOrigin())
disp.SetSpacing(disp_field.GetSpacing())
disp.SetDimensions(disp_field.GetSize())
arr = numpy_to_vtk(a.ravel(), deep=True, array_type=vtk.VTK_DOUBLE)
arr.SetNumberOfComponents(3)
arr.SetName("Displacement")
disp.GetPointData().SetVectors(arr)
#calculate the strain from displacement field
getStrain = vtk.vtkCellDerivatives()
getStrain.SetInputData(disp)
getStrain.SetTensorModeToComputeStrain()
getStrain.Update()
#add the strain tensor to the displacement field structured grid
strains = getStrain.GetOutput()
c2p = vtk.vtkCellDataToPointData()
c2p.PassCellDataOff()
c2p.SetInputData(strains)
c2p.Update()
disp = c2p.GetOutput()
#use VTK probe filter to interpolate displacements and strains
#to 3D meshes of cells and save as UnstructuredGrid (.vtu)
# to visualize in ParaView; this is a linear interpolation
print("...Interpolating displacements to 3D mesh.")
if self.rigidInitial:
#transform 3D Mesh
tf = vtk.vtkTransformFilter()
tf.SetInputData(mesh)
tf.SetTransform(self.rigidTransforms[r])
tf.Update()
mesh = tf.GetOutput()
probe = vtk.vtkProbeFilter()
probe.SetInputData(mesh)
probe.SetSourceData(disp)
probe.Update()
field = probe.GetOutput()
if self.display:
probe2 = vtk.vtkProbeFilter()
probe2.SetInputData(rpoly)
probe2.SetSourceData(disp)
probe2.Update()
self.cell_fields.append(field)
if self.saveFEA:
idisp = field.GetPointData().GetVectors()
bcs = np.zeros((len(self._snodes[r]), 3), float)
for j, node in enumerate(self._snodes[r]):
d = idisp.GetTuple3(node - 1)
bcs[j, 0] = d[0]
bcs[j, 1] = d[1]
bcs[j, 2] = d[2]
self._bcs.append(bcs)
idWriter = vtk.vtkXMLUnstructuredGridWriter()
idWriter.SetFileName(
str(
os.path.normpath(self._def_dir + os.sep +
'cell{:04d}.vtu'.format(r + 1))))
idWriter.SetInputData(self.cell_fields[r])
idWriter.Write()
if self.display:
self.animate(probe2.GetOutput(), r)
print("Registration completed.")
def vortmesh(args):
p = args[0]
cubenum = args[1]
print("Cube", cubenum)
#Check for additonal parameters
if (p["param1"] != ''):
comptype = p["param1"]
else:
comptype = "q" #Default to q criterion
if (p["param2"] != ''):
thresh = float(p["param2"])
else:
thresh = 783.3 #Default for q threshold on isotropic data
inputfile = p["inputfile"] + str(
cubenum) + ".npy" #Used so we can set either npy input or h5 input
outputfile = p["outputfile"] + str(
cubenum) + ".vtp" #always VTK Image Data for this.
sx = p["sx"]
sy = p["sy"]
sz = p["sz"]
ex = p["ex"]
ey = p["ey"]
ez = p["ez"]
print("Loading file, %s" % inputfile)
#Determine if file is h5 or numpy
rs = timeit.default_timer()
#In case file isn't here, catch this.
try:
vel = np.load(inputfile)
except:
p["message"] = "Failed to find file"
return p
re = timeit.default_timer()
#convert numpy array to vtk
cs = timeit.default_timer()
#convert numpy array to vtk
vtkdata = numpy_support.numpy_to_vtk(vel.flat,
deep=True,
array_type=vtk.VTK_FLOAT)
vtkdata.SetNumberOfComponents(3)
vtkdata.SetName("Velocity")
image = vtk.vtkImageData()
image.GetPointData().SetVectors(vtkdata)
image.SetExtent(sx, ex, sy, ey, sz, ez)
#NOTE: Hardcoding Spacing TODO: Add to parameters
image.SetSpacing(.006135923, .006135923, .006135923)
ce = timeit.default_timer()
vs = timeit.default_timer()
if (comptype == "v"):
vorticity = vtk.vtkCellDerivatives()
vorticity.SetVectorModeToComputeVorticity()
vorticity.SetTensorModeToPassTensors()
vorticity.SetInputData(image)
vorticity.Update()
elif (comptype == "q"):
vorticity = vtk.vtkGradientFilter()
vorticity.SetInputData(image)
vorticity.SetInputScalars(image.FIELD_ASSOCIATION_POINTS, "Velocity")
vorticity.ComputeQCriterionOn()
vorticity.SetComputeGradient(0)
vorticity.Update()
ve = timeit.default_timer()
#Generate contour for comparison
c = vtk.vtkContourFilter()
c.SetValue(0, thresh)
if (comptype == "q"):
image.GetPointData().SetScalars(
vorticity.GetOutput().GetPointData().GetVectors("Q-criterion"))
else:
image.GetPointData().SetScalars(
vorticity.GetOutput().GetPointData().GetVectors())
c.SetInputData(image)
c.Update()
w = vtk.vtkXMLPolyDataWriter()
w.SetEncodeAppendedData(0) #turn of base 64 encoding for fast write
w.SetFileName(outputfile)
w.SetInputData(c.GetOutput())
ws = timeit.default_timer()
result = w.Write()
we = timeit.default_timer()
print("Read time: %s" % str(re - rs))
print("Convert to vtk: %s" % str(ce - cs))
if (comptype == "q"):
print("Q Computation: %s" % str(ve - vs))
else:
print("Vorticity Computation: %s" % str(ve - vs))
print("Write %s" % str(we - ws))
print("Total time: %s" % str(we - rs))
if (result):
p["message"] = "Success"
p["computetime"] = str(we - rs)
return p #return the packet
