def mapDataSetToCellData(
mesh_from,
type_of_support,
mesh_to,
farray_names,
type_of_mapping="PointsWithinRadius",
radius_is_relative=True,
radius=0.5,
n_closest_points=3,
threshold_dist=None,
threshold_val_min=None,
threshold_val_max=None,
verbose=0):
myVTK.myPrint(verbose, "*** mapDataSetToCellData ***")
if (type_of_support == "point"):
datapoints = mesh_from.GetPoints()
dataset = mesh_from.GetPointData()
point_locator = myVTK.getPointLocator(
mesh_from,
verbose=verbose-1)
elif (type_of_support == "cell"):
datapoints = myVTK.getCellCenters(
mesh=mesh_from,
verbose=verbose-1)
dataset = mesh_from.GetCellData()
point_locator = myVTK.getPointLocator(
datapoints,
verbose=verbose-1)
else:
assert (0)
pdata_cell_centers_to = myVTK.getCellCenters(mesh_to)
n_cells = mesh_to.GetNumberOfCells()
farrays_avg = {}
farrays_std = {}
for farray_name in farray_names:
assert (dataset.HasArray(farray_name)), "mesh has no array named "+farray_name+". Aborting."
farray_type = dataset.GetArray(farray_name).GetDataTypeAsString()
farray_n_components = dataset.GetArray(farray_name).GetNumberOfComponents()
farrays_avg[farray_name] = myVTK.createArray(farray_name+"_avg",
farray_n_components,
n_cells,
farray_type)
farrays_std[farray_name] = myVTK.createArray(farray_name+"_std",
farray_n_components,
n_cells,
farray_type)
points_within_radius = vtk.vtkIdList()
for k_cell in xrange(n_cells):
if (type_of_mapping == "ClosestPoints"):
point_locator.FindClosestNPoints(
n_closest_points,
pdata_cell_centers_to.GetPoint(k_cell),
points_within_radius)
elif (type_of_mapping == "PointsWithinRadius"):
if (radius_is_relative):
l = (mesh_to.GetCell(k_cell).GetLength2())**(0.5)
actual_radius = l*radius
else:
actual_radius = radius
point_locator.FindPointsWithinRadius(
actual_radius,
pdata_cell_centers_to.GetPoint(k_cell),
points_within_radius)
else:
assert (0)
#points_within_radius = myVTK.findPointsInCell(mesh_from.GetPoints(), mesh_to.GetCell(k_cell))
for farray_name in farray_names:
if (points_within_radius.GetNumberOfIds()):
values = [numpy.array(dataset.GetArray(farray_name).GetTuple(points_within_radius.GetId(k_id))) for k_id in xrange(points_within_radius.GetNumberOfIds()) if (threshold_dist is None) or (numpy.linalg.norm(numpy.array(datapoints.GetPoint(points_within_radius.GetId(k_id)))-numpy.array(pdata_cell_centers_to.GetPoint(k_cell))) < threshold_dist)]
#print "values = "+str(values)
if (threshold_val_min != None):
values = [value for value in values if (numpy.linalg.norm(value) > threshold_val_min)]
if (threshold_val_max != None):
values = [value for value in values if (numpy.linalg.norm(value) < threshold_val_max)]
#print "values = "+str(values)
if (len(values)):
avg = numpy.mean(values, 0)
std = numpy.std(values, 0)
else:
avg = [0]*farray_n_components
std = [0]*farray_n_components
else:
avg = [0]*farray_n_components
std = [0]*farray_n_components
farrays_avg[farray_name].SetTuple(k_cell, avg)
farrays_std[farray_name].SetTuple(k_cell, std)
for farray_name in farray_names:
mesh_to.GetCellData().AddArray(farrays_avg[farray_name])
mesh_to.GetCellData().AddArray(farrays_std[farray_name])
def mapDataSetToCellData(mesh_from,
type_of_support,
mesh_to,
farray_names,
type_of_mapping="PointsWithinRadius",
radius_is_relative=True,
radius=0.5,
n_closest_points=3,
threshold_dist=None,
threshold_val_min=None,
threshold_val_max=None,
verbose=0):
myVTK.myPrint(verbose, "*** mapDataSetToCellData ***")
if (type_of_support == "point"):
datapoints = mesh_from.GetPoints()
dataset = mesh_from.GetPointData()
point_locator = myVTK.getPointLocator(mesh_from, verbose=verbose - 1)
elif (type_of_support == "cell"):
datapoints = myVTK.getCellCenters(mesh=mesh_from, verbose=verbose - 1)
dataset = mesh_from.GetCellData()
point_locator = myVTK.getPointLocator(datapoints, verbose=verbose - 1)
else:
assert (0)
pdata_cell_centers_to = myVTK.getCellCenters(mesh_to)
n_cells = mesh_to.GetNumberOfCells()
farrays_avg = {}
farrays_std = {}
for farray_name in farray_names:
assert (dataset.HasArray(farray_name)
), "mesh has no array named " + farray_name + ". Aborting."
farray_type = dataset.GetArray(farray_name).GetDataTypeAsString()
farray_n_components = dataset.GetArray(
farray_name).GetNumberOfComponents()
farrays_avg[farray_name] = myVTK.createArray(farray_name + "_avg",
farray_n_components,
n_cells, farray_type)
farrays_std[farray_name] = myVTK.createArray(farray_name + "_std",
farray_n_components,
n_cells, farray_type)
points_within_radius = vtk.vtkIdList()
for k_cell in xrange(n_cells):
if (type_of_mapping == "ClosestPoints"):
point_locator.FindClosestNPoints(
n_closest_points, pdata_cell_centers_to.GetPoint(k_cell),
points_within_radius)
elif (type_of_mapping == "PointsWithinRadius"):
if (radius_is_relative):
l = (mesh_to.GetCell(k_cell).GetLength2())**(0.5)
actual_radius = l * radius
else:
actual_radius = radius
point_locator.FindPointsWithinRadius(
actual_radius, pdata_cell_centers_to.GetPoint(k_cell),
points_within_radius)
else:
assert (0)
#points_within_radius = myVTK.findPointsInCell(mesh_from.GetPoints(), mesh_to.GetCell(k_cell))
for farray_name in farray_names:
if (points_within_radius.GetNumberOfIds()):
values = [
numpy.array(
dataset.GetArray(farray_name).GetTuple(
points_within_radius.GetId(k_id)))
for k_id in xrange(points_within_radius.GetNumberOfIds())
if (threshold_dist is None) or (numpy.linalg.norm(
numpy.array(
datapoints.GetPoint(
points_within_radius.GetId(k_id))) -
numpy.array(pdata_cell_centers_to.GetPoint(k_cell))) <
threshold_dist)
]
#print "values = "+str(values)
if (threshold_val_min != None):
values = [
value for value in values
if (numpy.linalg.norm(value) > threshold_val_min)
]
if (threshold_val_max != None):
values = [
value for value in values
if (numpy.linalg.norm(value) < threshold_val_max)
]
#print "values = "+str(values)
if (len(values)):
avg = numpy.mean(values, 0)
std = numpy.std(values, 0)
else:
avg = [0] * farray_n_components
std = [0] * farray_n_components
else:
avg = [0] * farray_n_components
std = [0] * farray_n_components
farrays_avg[farray_name].SetTuple(k_cell, avg)
farrays_std[farray_name].SetTuple(k_cell, std)
for farray_name in farray_names:
mesh_to.GetCellData().AddArray(farrays_avg[farray_name])
mesh_to.GetCellData().AddArray(farrays_std[farray_name])
def addMappingToPointData(mesh_from,
type_of_support,
mesh_to,
farray_names,
radius=1.,
threshold_min=None,
threshold_max=None,
verbose=0):
mypy.my_print(verbose, "*** addMappingToPointData ***")
if (type_of_support == "point"):
dataset = mesh_from.GetPointData()
point_locator = myvtk.getPointLocator(mesh_from)
elif (type_of_support == "cell"):
dataset = mesh_from.GetPointData()
pdata_cell_centers_fr = myvtk.getCellCenters(mesh=mesh_from,
verbose=verbose - 1)
point_locator = myvtk.getPointLocator(pdata_cell_centers_fr)
n_points = mesh_to.GetNumberOfPoints()
farrays_avg = {}
farrays_std = {}
farrays_rat = {}
for farray_name in farray_names:
assert (dataset.HasArray(farray_name)
), "mesh has no array named " + farray_name + ". Aborting."
farray_type = dataset.GetArray(farray_name).GetDataTypeAsString()
farray_n_components = dataset.GetArray(
farray_name).GetNumberOfComponents()
farrays_avg[farray_name] = createArray(farray_name + "_avg",
farray_n_components, n_points,
farray_type)
farrays_std[farray_name] = createArray(farray_name + "_std",
farray_n_components, n_points,
farray_type)
farrays_rat[farray_name] = createArray(farray_name + "_rat",
farray_n_components, n_points,
farray_type)
points_within_radius = vtk.vtkIdList()
for k_point in xrange(n_points):
#point_locator.FindClosestNPoints(
#3,
#mesh_to.GetPoints().GetPoint(k_point),
#points_within_radius)
point_locator.FindPointsWithinRadius(
radius,
mesh_to.GetPoints().GetPoint(k_point), points_within_radius)
for farray_name in farray_names:
if (points_within_radius.GetNumberOfIds() > 0):
values = [
numpy.array(
dataset.GetArray(farray_name).GetTuple(
points_within_radius.GetId(k_id)))
for k_id in xrange(points_within_radius.GetNumberOfIds())
]
#print "values = "+str(values)
if (threshold_min != None):
values = [
value for value in values
if (numpy.linalg.norm(value) > threshold_min)
]
if (threshold_max != None):
values = [
value for value in values
if (numpy.linalg.norm(value) < threshold_max)
]
#print "values = "+str(values)
if (len(values) > 0):
avg = numpy.mean(values, 0)
std = numpy.std(values, 0)
rat = std / avg
else:
avg = [0] * n_components
std = [0] * n_components
rat = [0] * n_components
else:
avg = [0] * n_components
std = [0] * n_components
rat = [0] * n_components
farrays_avg[farray_name].SetTuple(k_point, avg)
farrays_std[farray_name].SetTuple(k_point, std)
farrays_rat[farray_name].SetTuple(k_point, rat)
for farray_name in farray_names:
mesh_to.GetPointData().AddArray(farrays_avg[farray_name])
mesh_to.GetPointData().AddArray(farrays_std[farray_name])
mesh_to.GetPointData().AddArray(farrays_rat[farray_name])
def addVoxels(
ugrid,
verbose=1):
myVTK.myPrint(verbose, "*** addVoxels ***")
n_points = ugrid.GetPoints().GetNumberOfPoints()
seed_point = int(n_points/2)
point_locator = myVTK.getPointLocator(ugrid)
n_closest_points = 100
closest_points = vtk.vtkIdList()
point_locator.FindClosestNPoints(
n_closest_points,
ugrid.GetPoint(seed_point),
closest_points)
P0 = numpy.array(ugrid.GetPoint(closest_points.GetId(0)))
#print "P0 = " + str(P0)
P1 = numpy.array(ugrid.GetPoint(closest_points.GetId(1)))
#print "P1 = " + str(P1)
X = P1-P0
dX = numpy.linalg.norm(X)
X /= dX
#print "X = " + str(X)
#print "dX = " + str(dX)
for k_point in xrange(2, n_closest_points):
#print "k_point = " + str(k_point)
P2 = numpy.array(ugrid.GetPoint(closest_points.GetId(k_point)))
Y = P2-P0
dY = numpy.linalg.norm(Y)
Y /= dY
#print "P2 = " + str(P2)
#print "Y = " + str(Y)
#print "dY = " + str(dY)
#print "numpy.dot(Y, X) = " + str(numpy.dot(Y, X))
if (abs(numpy.dot(Y, X)) < 0.001):
Y = P2-P0
dY = numpy.linalg.norm(Y)
Y /= dY
break
#print "Y = " + str(Y)
#print "dY = " + str(dY)
Z = numpy.cross(X, Y)
dZ_list = []
for k_point in xrange(2, n_closest_points):
#print "k_point = " + str(k_point)
P3 = numpy.array(ugrid.GetPoint(closest_points.GetId(k_point)))
ZZ = P3-P0
dZ = numpy.linalg.norm(ZZ)
ZZ /= dZ
#print "P3 = " + str(P3)
#print "ZZ = " + str(ZZ)
#print "dZ = " + str(dZ)
#print "numpy.dot(ZZ, Z) = " + str(numpy.dot(ZZ, Z))
if (abs(numpy.dot(ZZ, Z)) > 0.999):
dZ_list.append(dZ)
dZ = min(dZ_list)
#print "Z = " + str(Z)
#print "dZ = " + str(dZ)
#print "numpy.dot(Y, X) = " + str(numpy.dot(Y, X))
#print "numpy.dot(Z, X) = " + str(numpy.dot(Z, X))
#print "numpy.dot(Z, Y) = " + str(numpy.dot(Z, Y))
points = vtk.vtkPoints()
point_locator = vtk.vtkPointLocator()
point_locator.InitPointInsertion(points, ugrid.GetBounds())
radius = min(dX, dY, dZ)/2
cell = vtk.vtkHexahedron()
cell_array = vtk.vtkCellArray()
for k_point in xrange(n_points):
P = numpy.array(ugrid.GetPoint(k_point))
point_ids = []
for pm_Z in [-1,+1]:
for pm_Y in [-1,+1]:
if (pm_Y == -1): pm_X_list = [-1,+1]
elif (pm_Y == +1): pm_X_list = [+1,-1]
for pm_X in pm_X_list:
PP = P + pm_Z * (dZ/2) * Z + pm_Y * (dY/2) * Y + pm_X * (dX/2) * X
if (points.GetNumberOfPoints() == 0):
point_id = point_locator.InsertNextPoint(PP)
else:
point_id = point_locator.FindClosestInsertedPoint(PP)
dist = numpy.linalg.norm(points.GetPoint(point_id)-PP)
if (dist > radius):
point_id = point_locator.InsertNextPoint(PP)
#point_id = point_locator.IsInsertedPoint(PP)
#if (point_id == -1):
#point_id = point_locator.InsertNextPoint(PP)
point_ids.append(point_id)
for i in xrange(8):
cell.GetPointIds().SetId(i, point_ids[i])
cell_array.InsertNextCell(cell)
new_ugrid = vtk.vtkUnstructuredGrid()
new_ugrid.SetPoints(points)
new_ugrid.SetCells(vtk.VTK_HEXAHEDRON, cell_array)
n_arrays = ugrid.GetPointData().GetNumberOfArrays()
for k_array in xrange(n_arrays):
new_ugrid.GetCellData().AddArray(ugrid.GetPointData().GetArray(k_array))
return new_ugrid
def getVoxels(ugrid, verbose=0):
mypy.my_print(verbose, "*** getVoxels ***")
n_points = ugrid.GetPoints().GetNumberOfPoints()
seed_point = int(n_points / 2)
point_locator = myvtk.getPointLocator(ugrid)
n_closest_points = 100
closest_points = vtk.vtkIdList()
point_locator.FindClosestNPoints(n_closest_points,
ugrid.GetPoint(seed_point),
closest_points)
P0 = numpy.empty(3)
P1 = numpy.empty(3)
P2 = numpy.empty(3)
P3 = numpy.empty(3)
ugrid.GetPoint(closest_points.GetId(0), P0)
#print "P0 = "+str(P0)
ugrid.GetPoint(closest_points.GetId(1), P1)
#print "P1 = "+str(P1)
X = P1 - P0
dX = numpy.linalg.norm(X)
X /= dX
#print "X = "+str(X)
#print "dX = "+str(dX)
for k_point in xrange(2, n_closest_points):
#print "k_point = "+str(k_point)
ugrid.GetPoint(closest_points.GetId(k_point), P2)
Y = P2 - P0
dY = numpy.linalg.norm(Y)
Y /= dY
#print "P2 = "+str(P2)
#print "Y = "+str(Y)
#print "dY = "+str(dY)
#print "numpy.dot(Y, X) = "+str(numpy.dot(Y, X))
if (abs(numpy.dot(Y, X)) < 0.001):
Y = P2 - P0
dY = numpy.linalg.norm(Y)
Y /= dY
break
#print "Y = "+str(Y)
#print "dY = "+str(dY)
Z = numpy.cross(X, Y)
dZ_list = []
for k_point in xrange(2, n_closest_points):
#print "k_point = "+str(k_point)
ugrid.GetPoint(closest_points.GetId(k_point), P3)
ZZ = P3 - P0
dZ = numpy.linalg.norm(ZZ)
ZZ /= dZ
#print "P3 = "+str(P3)
#print "ZZ = "+str(ZZ)
#print "dZ = "+str(dZ)
#print "numpy.dot(ZZ, Z) = "+str(numpy.dot(ZZ, Z))
if (abs(numpy.dot(ZZ, Z)) > 0.999):
dZ_list.append(dZ)
dZ = min(dZ_list)
#print "Z = "+str(Z)
#print "dZ = "+str(dZ)
#print "numpy.dot(Y, X) = "+str(numpy.dot(Y, X))
#print "numpy.dot(Z, X) = "+str(numpy.dot(Z, X))
#print "numpy.dot(Z, Y) = "+str(numpy.dot(Z, Y))
points = vtk.vtkPoints()
point_locator = vtk.vtkPointLocator()
point_locator.InitPointInsertion(points, ugrid.GetBounds())
radius = min(dX, dY, dZ) / 2
cell = vtk.vtkHexahedron()
cell_array = vtk.vtkCellArray()
P = numpy.empty(3)
PPP = numpy.empty(3)
for k_point in xrange(n_points):
ugrid.GetPoint(k_point, P)
point_ids = []
for pm_Z in [-1, +1]:
for pm_Y in [-1, +1]:
if (pm_Y == -1): pm_X_list = [-1, +1]
elif (pm_Y == +1): pm_X_list = [+1, -1]
for pm_X in pm_X_list:
PP = P + pm_Z * (dZ / 2) * Z + pm_Y * (
dY / 2) * Y + pm_X * (dX / 2) * X
if (points.GetNumberOfPoints() == 0):
point_id = point_locator.InsertNextPoint(PP)
else:
point_id = point_locator.FindClosestInsertedPoint(PP)
points.GetPoint(point_id, PPP)
dist = numpy.linalg.norm(PPP - PP)
if (dist > radius):
point_id = point_locator.InsertNextPoint(PP)
#point_id = point_locator.IsInsertedPoint(PP)
#if (point_id == -1):
#point_id = point_locator.InsertNextPoint(PP)
point_ids.append(point_id)
for i in xrange(8):
cell.GetPointIds().SetId(i, point_ids[i])
cell_array.InsertNextCell(cell)
new_ugrid = vtk.vtkUnstructuredGrid()
new_ugrid.SetPoints(points)
new_ugrid.SetCells(vtk.VTK_HEXAHEDRON, cell_array)
n_arrays = ugrid.GetPointData().GetNumberOfArrays()
for k_array in xrange(n_arrays):
new_ugrid.GetCellData().AddArray(
ugrid.GetPointData().GetArray(k_array))
return new_ugrid
