def getThresholdedUGrid(
ugrid,
field_support,
field_name,
threshold_value,
threshold_by_upper_or_lower,
verbose=0):
mypy.my_print(verbose, "*** getThresholdedUGrid ***")
threshold = vtk.vtkThreshold()
if (vtk.vtkVersion.GetVTKMajorVersion() >= 6):
threshold.SetInputData(ugrid)
else:
threshold.SetInput(ugrid)
if (field_support == "points"):
association = vtk.vtkDataObject.FIELD_ASSOCIATION_POINTS
elif (field_support == "cells"):
association = vtk.vtkDataObject.FIELD_ASSOCIATION_CELLS
threshold.SetInputArrayToProcess(0, 0, 0, association, field_name)
if (threshold_by_upper_or_lower == "upper"):
threshold.ThresholdByUpper(threshold_value)
elif (threshold_by_upper_or_lower == "lower"):
threshold.ThresholdByLower(threshold_value)
threshold.Update()
thresholded_ugrid = threshold.GetOutput()
return thresholded_ugrid
def readDynaDeformationGradients(
mesh,
hystory_files_basename,
array_name,
verbose=0):
mypy.my_print(verbose, "*** readDynaDeformationGradients ***")
n_cells = mesh.GetNumberOfCells()
history_files_names = [hystory_files_basename + '.history#' + str(num) for num in xrange(11,20)]
F_list = [[0. for k_component in xrange(9)] for k_cell in xrange(n_cells)]
for k_component in xrange(9):
history_file = open(history_files_names[k_component], 'r')
for line in history_file:
if line.startswith('*') or line.startswith('$'): continue
line = line.split()
F_list[int(line[0])-1][k_component] = float(line[1])
history_file.close()
F_array = myvtk.createFloatArray(array_name, 9, n_cells)
for k_cell in xrange(n_cells):
F_array.SetTuple(k_cell, F_list[k_cell])
mypy.my_print(verbose-1, "n_tuples = "+str(F_array.GetNumberOfTuples()))
mesh.GetCellData().AddArray(F_array)
def addPhysicalGroupToMesh(
mesh,
msh_filename,
verbose=0):
mypy.my_print(verbose, "*** addPhysicalGroupToMesh ***")
n_cells = mesh.GetNumberOfCells()
iarray_part_id = myVTK.createIntArray(
name="part_id",
n_tuples=n_cells,
n_components=1)
mesh.GetCellData().AddArray(iarray_part_id)
msh = open(msh_filename)
context = ""
for line in msh:
if line.startswith("$Elements"):
context = "reading element number"
continue
elif line.startswith("$EndElements"):
context = ""
continue
if (context == "reading elements"):
splitted_line = line.split()
iarray_part_id.SetTuple(int(splitted_line[0])-1, [int(splitted_line[3])-1])
elif (context == "reading element number"):
n_elements = int(line)
assert (n_elements == n_cells)
context = "reading elements"
def getThresholdedUGrid(
ugrid,
field_support,
field_name,
threshold_value,
threshold_by_upper_or_lower,
verbose=0):
mypy.my_print(verbose, "*** getThresholdedUGrid ***")
threshold = vtk.vtkThreshold()
if (vtk.vtkVersion.GetVTKMajorVersion() >= 6):
threshold.SetInputData(ugrid)
else:
threshold.SetInput(ugrid)
if (field_support == "points"):
association = vtk.vtkDataObject.FIELD_ASSOCIATION_POINTS
elif (field_support == "cells"):
association = vtk.vtkDataObject.FIELD_ASSOCIATION_CELLS
threshold.SetInputArrayToProcess(0, 0, 0, association, field_name)
if (threshold_by_upper_or_lower == "upper"):
threshold.ThresholdByUpper(threshold_value)
elif (threshold_by_upper_or_lower == "lower"):
threshold.ThresholdByLower(threshold_value)
threshold.Update()
thresholded_ugrid = threshold.GetOutput()
return thresholded_ugrid
def readAbaqusDeformationGradientsFromDAT(
data_filename,
verbose=0):
mypy.my_print(verbose, "*** readAbaqusDeformationGradientsFromDAT: "+data_filename+" ***")
farray_F = myvtk.createFloatArray("F", 9)
data_file = open(data_filename, 'r')
context = ""
k_cell = 0
for line in data_file:
if (context == "reading deformation gradients"):
#print line
if ("MAXIMUM" in line):
context = ""
continue
if ("OR" in line):
splitted_line = line.split()
assert (int(splitted_line[0]) == k_cell+1), "Wrong element number. Aborting."
F_list = [float(splitted_line[ 3]), float(splitted_line[ 6]), float(splitted_line[7]),
float(splitted_line[ 9]), float(splitted_line[ 4]), float(splitted_line[8]),
float(splitted_line[10]), float(splitted_line[11]), float(splitted_line[5])]
farray_F.InsertNextTuple(F_list)
k_cell += 1
if (line == " ELEMENT PT FOOT- DG11 DG22 DG33 DG12 DG13 DG23 DG21 DG31 DG32 \n"):
context = "reading deformation gradients"
data_file.close()
mypy.my_print(verbose-1, "n_tuples = "+str(farray_F.GetNumberOfTuples()))
return farray_F
def subArrays(
array1,
array2,
array3=None,
verbose=0):
mypy.my_print(verbose, "*** subArrays ***")
n_components = array1.GetNumberOfComponents()
assert (array2.GetNumberOfComponents() == n_components)
n_tuples = array1.GetNumberOfTuples()
assert (array2.GetNumberOfTuples() == n_tuples)
array_type = type(array1.GetTuple(0)[0])
assert (array_type in [int, float])
assert (type(array2.GetTuple(0)[0]) is array_type)
if (array3 is None):
array3 = myvtk.createArray(
name="",
n_components=n_components,
n_tuples=n_tuples,
array_type=array_type)
else:
assert (array3.GetNumberOfComponents() == n_components)
assert (array3.GetNumberOfTuples() == n_tuples)
assert (type(array3.GetTuple(0)[0]) is array_type)
for k_tuple in xrange(n_tuples):
array3.SetTuple(
k_tuple,
numpy.array(array1.GetTuple(k_tuple)) - numpy.array(array2.GetTuple(k_tuple)))
return array3
def getPDataSurfaceArea(pdata, verbose=0):
mypy.my_print(verbose, "*** getPDataSurfaceArea ***")
mass_properties = myvtk.getMassProperties(pdata=pdata, verbose=verbose - 1)
return mass_properties.GetSurfaceArea()
def addMappingFromPointsToCells(ugrid_points, ugrid_cells, verbose=0):
mypy.my_print(verbose, "*** addMappingFromPointsToCells ***")
n_points = ugrid_points.GetNumberOfPoints()
n_cells = ugrid_cells.GetNumberOfCells()
#print "n_points = "+str(n_points)
#print "n_cells = "+str(n_cells)
(cell_locator, closest_point, generic_cell, k_cell, subId,
dist) = getCellLocator(mesh=ugrid_cells, verbose=verbose - 1)
iarray_k_cell = createIntArray(name="k_cell",
n_components=1,
n_tuples=n_points,
verbose=verbose - 1)
ugrid_points.GetPointData().AddArray(iarray_k_cell)
ugrid_points.GetCellData().AddArray(iarray_k_cell)
point = numpy.empty(3)
for k_point in xrange(n_points):
ugrid_points.GetPoint(k_point, point)
cell_locator.FindClosestPoint(point, closest_point, generic_cell,
k_cell, subId, dist)
#k_cell = cell_locator.FindCell(point)
#print "k_point = "+str(k_point)
#print "k_cell = "+str(k_cell)
iarray_k_cell.SetTuple1(k_point, k_cell)
def subArrays(
array1,
array2,
array3=None,
verbose=0):
mypy.my_print(verbose, "*** subArrays ***")
n_components = array1.GetNumberOfComponents()
assert (array2.GetNumberOfComponents() == n_components)
n_tuples = array1.GetNumberOfTuples()
assert (array2.GetNumberOfTuples() == n_tuples)
array_type = type(array1.GetTuple(0)[0])
assert (array_type in [int, float])
assert (type(array2.GetTuple(0)[0]) is array_type)
if (array3 is None):
array3 = myvtk.createArray(
name="",
n_components=n_components,
n_tuples=n_tuples,
array_type=array_type)
else:
assert (array3.GetNumberOfComponents() == n_components)
assert (array3.GetNumberOfTuples() == n_tuples)
assert (type(array3.GetTuple(0)[0]) is array_type)
for k_tuple in xrange(n_tuples):
array3.SetTuple(
k_tuple,
numpy.array(array1.GetTuple(k_tuple)) - numpy.array(array2.GetTuple(k_tuple)))
return array3
def readDynaDeformationGradients(mesh,
hystory_files_basename,
array_name,
verbose=0):
mypy.my_print(verbose, "*** readDynaDeformationGradients ***")
n_cells = mesh.GetNumberOfCells()
history_files_names = [
hystory_files_basename + ".history#" + str(num)
for num in range(11, 20)
]
F_list = [[0. for k_component in range(9)] for k_cell in range(n_cells)]
for k_component in range(9):
history_file = open(history_files_names[k_component], "r")
for line in history_file:
if line.startswith("*") or line.startswith("$"): continue
line = line.split()
F_list[int(line[0]) - 1][k_component] = float(line[1])
history_file.close()
F_array = myvtk.createFloatArray(array_name, 9, n_cells)
for k_cell in range(n_cells):
F_array.SetTuple(k_cell, F_list[k_cell])
mypy.my_print(verbose - 1,
"n_tuples = " + str(F_array.GetNumberOfTuples()))
mesh.GetCellData().AddArray(F_array)
def ugrid2pdata(
ugrid,
only_trianlges=False,
verbose=0):
mypy.my_print(verbose, "*** ugrid2pdata ***")
filter_geometry = vtk.vtkGeometryFilter()
if (vtk.vtkVersion.GetVTKMajorVersion() >= 6):
filter_geometry.SetInputData(ugrid)
else:
filter_geometry.SetInput(ugrid)
filter_geometry.Update()
pdata = filter_geometry.GetOutput()
if (only_trianlges):
filter_triangle = vtk.vtkTriangleFilter()
if (vtk.vtkVersion.GetVTKMajorVersion() >= 6):
filter_triangle.SetInputData(pdata)
else:
filter_triangle.SetInput(pdata)
filter_triangle.Update()
pdata = filter_triangle.GetOutput()
return pdata
def readAbaqusStressFromDAT(data_filename, verbose=0):
mypy.my_print(verbose,
"*** readAbaqusStressFromDAT: " + data_filename + " ***")
s_array = myvtk.createFloatArray("", 6)
data_file = open(data_filename, 'r')
context = ""
k_cell = 0
for line in data_file:
if (context == "reading stresses"):
#print line
if ("MAXIMUM" in line):
context = ""
continue
if ("OR" in line):
splitted_line = line.split()
assert (int(splitted_line[0]) == k_cell +
1), "Wrong element number. Aborting."
s_list = [float(splitted_line[k]) for k in xrange(3, 9)]
s_array.InsertNextTuple(s_list)
k_cell += 1
if (line ==
" ELEMENT PT FOOT- S11 S22 S33 S12 S13 S23 \n"
):
context = "reading stresses"
data_file.close()
mypy.my_print(verbose - 1,
"n_tuples = " + str(s_array.GetNumberOfTuples()))
return s_array
def readAbaqusDeformationGradientsFromDAT(
data_filename,
verbose=0):
mypy.my_print(verbose, "*** readAbaqusDeformationGradientsFromDAT: "+data_filename+" ***")
farray_F = myvtk.createFloatArray("F", 9)
data_file = open(data_filename, "r")
context = ""
k_cell = 0
for line in data_file:
if (context == "reading deformation gradients"):
#print line
if ("MAXIMUM" in line):
context = ""
continue
if ("OR" in line):
splitted_line = line.split()
assert (int(splitted_line[0]) == k_cell+1), "Wrong element number. Aborting."
F_list = [float(splitted_line[ 3]), float(splitted_line[ 6]), float(splitted_line[7]),
float(splitted_line[ 9]), float(splitted_line[ 4]), float(splitted_line[8]),
float(splitted_line[10]), float(splitted_line[11]), float(splitted_line[5])]
farray_F.InsertNextTuple(F_list)
k_cell += 1
if (line == " ELEMENT PT FOOT- DG11 DG22 DG33 DG12 DG13 DG23 DG21 DG31 DG32 \n"):
context = "reading deformation gradients"
data_file.close()
mypy.my_print(verbose-1, "n_tuples = "+str(farray_F.GetNumberOfTuples()))
return farray_F
def moveMeshWithWorldMatrix(mesh, M, in_place=True, verbose=0):
mypy.my_print(verbose, "*** moveMeshWithWorldMatrix ***")
if (in_place):
mesh2 = mesh
else:
if mesh.IsA("vtkPolyData"):
mesh2 = vtk.vtkPolyData()
elif mesh.IsA("vtkUnstructuredGrid"):
mesh2 = vtk.vtkUnstructuredGrid()
else:
assert (0), "Not implemented. Aborting."
mesh2.DeepCopy(mesh)
n_points = mesh2.GetNumberOfPoints()
points = mesh2.GetPoints()
P = numpy.empty(4)
P[3] = 1.
Q = numpy.empty(4)
for k_point in range(n_points):
P[0:3] = points.GetPoint(k_point)
#print P
Q = numpy.dot(M, P)
#print Q
points.SetPoint(k_point, Q[0:3])
return mesh2
def getClippedPDataUsingPlane(pdata_mesh, plane_O, plane_N, verbose=0):
mypy.my_print(verbose, "*** getClippedPDataUsingPlane ***")
plane = vtk.vtkPlane()
plane.SetOrigin(plane_O)
plane.SetNormal(plane_N)
#mypy.my_print(verbose-1, "pdata_mesh.GetBounds() = "+str(pdata_mesh.GetBounds()))
#mypy.my_print(verbose-1, "plane_O = "+str(plane_O))
#mypy.my_print(verbose-1, "plane_N = "+str(plane_N))
clip = vtk.vtkClipPolyData()
clip.SetClipFunction(plane)
clip.GenerateClippedOutputOn()
if (vtk.vtkVersion.GetVTKMajorVersion() >= 6):
clip.SetInputData(pdata_mesh)
else:
clip.SetInput(pdata_mesh)
clip.Update()
clipped0 = clip.GetOutput(0)
clipped1 = clip.GetOutput(1)
#mypy.my_print(verbose-1, "clipped0.GetNumberOfPoints() = "+str(clipped0.GetNumberOfPoints()))
#mypy.my_print(verbose-1, "clipped1.GetNumberOfPoints() = "+str(clipped1.GetNumberOfPoints()))
#mypy.my_print(verbose-1, "clipped0.GetNumberOfCells() = "+str(clipped0.GetNumberOfCells()))
#mypy.my_print(verbose-1, "clipped1.GetNumberOfCells() = "+str(clipped1.GetNumberOfCells()))
if (clipped0.GetNumberOfCells() > clipped1.GetNumberOfCells()):
return clipped0, clipped1
else:
return clipped1, clipped0
def getMassProperties(pdata, verbose=0):
mypy.my_print(verbose, "*** getMassProperties ***")
mass_properties = vtk.vtkMassProperties()
if (vtk.vtkVersion.GetVTKMajorVersion() >= 6):
mass_properties.SetInputData(pdata)
else:
mass_properties.SetInput(pdata)
return mass_properties
def getPointLocator(
mesh,
verbose=0):
mypy.my_print(verbose, "*** getPointLocator ***")
point_locator = vtk.vtkPointLocator()
point_locator.SetDataSet(mesh)
point_locator.Update()
return point_locator
def getPointLocator(
mesh,
verbose=0):
mypy.my_print(verbose, "*** getPointLocator ***")
point_locator = vtk.vtkPointLocator()
point_locator.SetDataSet(mesh)
point_locator.Update()
return point_locator
def getPDataSurfaceArea(
pdata,
verbose=0):
mypy.my_print(verbose, "*** getPDataSurfaceArea ***")
mass_properties = myvtk.getMassProperties(
pdata=pdata,
verbose=verbose-1)
return mass_properties.GetSurfaceArea()
def writeSTL(pdata, filename, verbose=0):
mypy.my_print(verbose, "*** writeSTL: " + filename + " ***")
stl_writer = vtk.vtkSTLWriter()
stl_writer.SetFileName(filename)
if (vtk.vtkVersion.GetVTKMajorVersion() >= 6):
stl_writer.SetInputData(pdata)
else:
stl_writer.SetInput(pdata)
stl_writer.Update()
stl_writer.Write()
def addImageHessian(
image,
image_dimensionality=None,
verbose=0):
mypy.my_print(verbose, "*** addImageHessian ***")
if (image_dimensionality is None):
image_dimensionality = myvtk.getImageDimensionality(
image=image,
verbose=verbose-1)
image_gradient = vtk.vtkImageGradient()
if (vtk.vtkVersion.GetVTKMajorVersion() >= 6):
image_gradient.SetInputData(image)
else:
image_gradient.SetInput(image)
image_gradient.SetDimensionality(image_dimensionality)
image_gradient.Update()
image_w_gradient = image_gradient.GetOutput()
image_append_components = vtk.vtkImageAppendComponents()
for k_dim in xrange(image_dimensionality):
image_extract_components = vtk.vtkImageExtractComponents()
if (vtk.vtkVersion.GetVTKMajorVersion() >= 6):
image_extract_components.SetInputData(image_w_gradient)
else:
image_extract_components.SetInput(image_w_gradient)
image_extract_components.SetComponents(k_dim)
image_extract_components.Update()
image_w_gradient_component = image_extract_components.GetOutput()
image_gradient = vtk.vtkImageGradient()
if (vtk.vtkVersion.GetVTKMajorVersion() >= 6):
image_gradient.SetInputData(image_w_gradient_component)
else:
image_gradient.SetInput(image_w_gradient_component)
image_gradient.SetDimensionality(image_dimensionality)
image_gradient.Update()
image_w_hessian_component = image_gradient.GetOutput()
if (vtk.vtkVersion.GetVTKMajorVersion() >= 6):
image_append_components.AddInputData(image_w_hessian_component)
else:
image_append_components.AddInput(image_w_hessian_component)
image_append_components.Update()
image_w_hessian = image_append_components.GetOutput()
name = image.GetPointData().GetScalars().GetName()
image.GetPointData().AddArray(image_w_gradient.GetPointData().GetArray(name+"Gradient"))
image.GetPointData().AddArray(image_w_hessian.GetPointData().GetArray(name+"GradientGradient"))
image.GetPointData().SetActiveScalars(name+"GradientGradient")
def getCellCenters(mesh, verbose=0):
mypy.my_print(verbose, "*** getCellCenters ***")
filter_cell_centers = vtk.vtkCellCenters()
if (vtk.vtkVersion.GetVTKMajorVersion() >= 6):
filter_cell_centers.SetInputData(mesh)
else:
filter_cell_centers.SetInput(mesh)
filter_cell_centers.Update()
cell_centers = filter_cell_centers.GetOutput()
return cell_centers
def getMassProperties(
pdata,
verbose=0):
mypy.my_print(verbose, "*** getMassProperties ***")
mass_properties = vtk.vtkMassProperties()
if (vtk.vtkVersion.GetVTKMajorVersion() >= 6):
mass_properties.SetInputData(pdata)
else:
mass_properties.SetInput(pdata)
return mass_properties
def pdata2ugrid(pdata, verbose=0):
mypy.my_print(verbose, "*** pdata2ugrid ***")
filter_append = vtk.vtkAppendFilter()
if vtk.vtkVersion.GetVTKMajorVersion() >= 6:
filter_append.SetInputData(pdata)
else:
filter_append.SetInput(pdata)
filter_append.Update()
ugrid = filter_append.GetOutput()
return ugrid
def pdata2ugrid(pdata, verbose=0):
mypy.my_print(verbose, "*** pdata2ugrid ***")
filter_append = vtk.vtkAppendFilter()
if (vtk.vtkVersion.GetVTKMajorVersion() >= 6):
filter_append.SetInputData(pdata)
else:
filter_append.SetInput(pdata)
filter_append.Update()
ugrid = filter_append.GetOutput()
return ugrid
def addImageHessian(image, image_dimensionality=None, verbose=0):
mypy.my_print(verbose, "*** addImageHessian ***")
if (image_dimensionality is None):
image_dimensionality = myvtk.getImageDimensionality(image=image,
verbose=verbose -
1)
image_gradient = vtk.vtkImageGradient()
if (vtk.vtkVersion.GetVTKMajorVersion() >= 6):
image_gradient.SetInputData(image)
else:
image_gradient.SetInput(image)
image_gradient.SetDimensionality(image_dimensionality)
image_gradient.Update()
image_w_gradient = image_gradient.GetOutput()
image_append_components = vtk.vtkImageAppendComponents()
for k_dim in xrange(image_dimensionality):
image_extract_components = vtk.vtkImageExtractComponents()
if (vtk.vtkVersion.GetVTKMajorVersion() >= 6):
image_extract_components.SetInputData(image_w_gradient)
else:
image_extract_components.SetInput(image_w_gradient)
image_extract_components.SetComponents(k_dim)
image_extract_components.Update()
image_w_gradient_component = image_extract_components.GetOutput()
image_gradient = vtk.vtkImageGradient()
if (vtk.vtkVersion.GetVTKMajorVersion() >= 6):
image_gradient.SetInputData(image_w_gradient_component)
else:
image_gradient.SetInput(image_w_gradient_component)
image_gradient.SetDimensionality(image_dimensionality)
image_gradient.Update()
image_w_hessian_component = image_gradient.GetOutput()
if (vtk.vtkVersion.GetVTKMajorVersion() >= 6):
image_append_components.AddInputData(image_w_hessian_component)
else:
image_append_components.AddInput(image_w_hessian_component)
image_append_components.Update()
image_w_hessian = image_append_components.GetOutput()
name = image.GetPointData().GetScalars().GetName()
image.GetPointData().AddArray(
image_w_gradient.GetPointData().GetArray(name + "Gradient"))
image.GetPointData().AddArray(
image_w_hessian.GetPointData().GetArray(name + "GradientGradient"))
image.GetPointData().SetActiveScalars(name + "GradientGradient")
def addMappingFromPointsToCells(
ugrid_points,
ugrid_cells,
verbose=0):
mypy.my_print(verbose, "*** addMappingFromPointsToCells ***")
n_points = ugrid_points.GetNumberOfPoints()
n_cells = ugrid_cells.GetNumberOfCells()
#print "n_points = "+str(n_points)
#print "n_cells = "+str(n_cells)
(cell_locator,
closest_point,
generic_cell,
k_cell,
subId,
dist) = getCellLocator(
mesh=ugrid_cells,
verbose=verbose-1)
iarray_k_cell = createIntArray(
name="k_cell",
n_components=1,
n_tuples=n_points,
verbose=verbose-1)
ugrid_points.GetPointData().AddArray(iarray_k_cell)
ugrid_points.GetCellData().AddArray(iarray_k_cell)
point = numpy.empty(3)
for k_point in xrange(n_points):
ugrid_points.GetPoint(
k_point,
point)
cell_locator.FindClosestPoint(
point,
closest_point,
generic_cell,
k_cell,
subId,
dist)
#k_cell = cell_locator.FindCell(point)
#print "k_point = "+str(k_point)
#print "k_cell = "+str(k_cell)
iarray_k_cell.SetTuple1(
k_point,
k_cell)
def rotatePointsWithCenterAndRotationMatrix(points, C, R, verbose=0):
mypy.my_print(verbose, "*** rotatePointsWithCenterAndRotationMatrix ***")
n_points = points.GetNumberOfPoints()
point = numpy.empty(3)
for k_point in range(n_points):
points.GetPoint(k_point, point)
#print point
point = C + numpy.dot(R, point - C)
#print new_point
points.SetPoint(k_point, point)
def readPNG(filename, verbose=0):
mypy.my_print(verbose, "*** readPNG: " + filename + " ***")
assert (os.path.isfile(filename)
), "Wrong filename (\"" + filename + "\"). Aborting."
image_reader = vtk.vtkPNGReader()
image_reader.SetFileName(filename)
image_reader.Update()
image = image_reader.GetOutput()
mypy.my_print(verbose - 1, "n_points = " + str(image.GetNumberOfPoints()))
return image
def getCellLocator(mesh, verbose=0):
mypy.my_print(verbose, "*** getCellLocator ***")
cell_locator = vtk.vtkCellLocator()
cell_locator.SetDataSet(mesh)
cell_locator.Update()
closest_point = [0.] * 3
generic_cell = vtk.vtkGenericCell()
k_cell = vtk.mutable(0)
subId = vtk.mutable(0)
dist = vtk.mutable(0.)
return (cell_locator, closest_point, generic_cell, k_cell, subId, dist)
def getThresholdedPData(pdata,
field_support,
field_name,
threshold_value,
threshold_by_upper_or_lower,
verbose=0):
mypy.my_print(verbose, "*** getThresholdedPData ***")
thresholded_ugrid = getThresholdedUGrid(pdata, field_support, field_name,
threshold_value,
threshold_by_upper_or_lower, False)
thresholded_pdata = ugrid2pdata(thresholded_ugrid, False)
return thresholded_pdata
def writeSTL(
pdata,
filename,
verbose=0):
mypy.my_print(verbose, "*** writeSTL: "+filename+" ***")
stl_writer = vtk.vtkSTLWriter()
stl_writer.SetFileName(filename)
if (vtk.vtkVersion.GetVTKMajorVersion() >= 6):
stl_writer.SetInputData(pdata)
else:
stl_writer.SetInput(pdata)
stl_writer.Update()
stl_writer.Write()
def getCellCenters(
mesh,
verbose=0):
mypy.my_print(verbose, "*** getCellCenters ***")
filter_cell_centers = vtk.vtkCellCenters()
if (vtk.vtkVersion.GetVTKMajorVersion() >= 6):
filter_cell_centers.SetInputData(mesh)
else:
filter_cell_centers.SetInput(mesh)
filter_cell_centers.Update()
cell_centers = filter_cell_centers.GetOutput()
return cell_centers
def getClippedPDataUsingField(pdata_mesh, array_name, threshold_value, verbose=0):
mypy.my_print(verbose, "*** getClippedPDataUsingField ***")
pdata_mesh.GetPointData().SetActiveScalars(array_name)
clip_poly_data = vtk.vtkClipPolyData()
if vtk.vtkVersion.GetVTKMajorVersion() >= 6:
clip_poly_data.SetInputData(pdata_mesh)
else:
clip_poly_data.SetInput(pdata_mesh)
clip_poly_data.SetValue(threshold_value)
clip_poly_data.GenerateClippedOutputOn()
clip_poly_data.Update()
return clip_poly_data.GetOutput(0), clip_poly_data.GetOutput(1)
def getMaskedImageUsingMesh(
image,
mesh,
filter_with_field=None,
verbose=0):
mypy.my_print(verbose, "*** getMaskedImageUsingMesh ***")
n_points = image.GetNumberOfPoints()
farray_scalars_image = image.GetPointData().GetArray("scalars") # note that the field is defined at the points, not the cells
(cell_locator,
closest_point,
generic_cell,
k_cell,
subId,
dist) = myvtk.getCellLocator(
mesh=mesh,
verbose=verbose-1)
if (filter_with_field != None):
field = mesh.GetCellData().GetArray(filter_with_field[0])
field_values = filter_with_field[1]
points = vtk.vtkPoints()
farray_scalars = myvtk.createFloatArray(
name="scalars",
n_components=1)
point = numpy.empty(3)
for k_point in xrange(n_points):
image.GetPoint(k_point, point)
k_cell = cell_locator.FindCell(point)
if (k_cell == -1): continue
if (filter_with_field != None) and (field.GetTuple1(k_cell) not in field_values): continue
points.InsertNextPoint(point)
farray_scalars.InsertNextTuple(farray_scalars_image.GetTuple(k_point))
ugrid = vtk.vtkUnstructuredGrid()
ugrid.SetPoints(points)
ugrid.GetPointData().AddArray(farray_scalars)
myvtk.addVertices(
ugrid)
return ugrid
def getMaskedImageUsingMesh(
image,
mesh,
filter_with_field=None,
verbose=0):
mypy.my_print(verbose, "*** getMaskedImageUsingMesh ***")
n_points = image.GetNumberOfPoints()
farray_scalars_image = image.GetPointData().GetArray("scalars") # note that the field is defined at the points, not the cells
(cell_locator,
closest_point,
generic_cell,
k_cell,
subId,
dist) = myvtk.getCellLocator(
mesh=mesh,
verbose=verbose-1)
if (filter_with_field != None):
field = mesh.GetCellData().GetArray(filter_with_field[0])
field_values = filter_with_field[1]
points = vtk.vtkPoints()
farray_scalars = myvtk.createFloatArray(
name="scalars",
n_components=1)
point = numpy.empty(3)
for k_point in range(n_points):
image.GetPoint(k_point, point)
k_cell = cell_locator.FindCell(point)
if (k_cell == -1): continue
if (filter_with_field != None) and (field.GetTuple1(k_cell) not in field_values): continue
points.InsertNextPoint(point)
farray_scalars.InsertNextTuple(farray_scalars_image.GetTuple(k_point))
ugrid = vtk.vtkUnstructuredGrid()
ugrid.SetPoints(points)
ugrid.GetPointData().AddArray(farray_scalars)
myvtk.addVertices(
ugrid)
return ugrid
def rotateVectorArray(old_array,
in_vecs=None,
R=None,
out_vecs=None,
verbose=0):
mypy.my_print(verbose, "*** rotateVectorArray ***")
n_components = old_array.GetNumberOfComponents()
assert (
n_components == 3), "Wrong number of components (n_components=" + str(
n_components) + ", should be 3). Aborting."
n_tuples = old_array.GetNumberOfTuples()
new_array = myvtk.createFloatArray(old_array.GetName(), 3, n_tuples)
new_vector = numpy.empty(3)
old_vector = numpy.empty(3)
for k_tuple in range(n_tuples):
old_array.GetTuple(k_tuple, old_vector)
if (in_vecs is None):
in_R = numpy.eye(3)
else:
in_R = numpy.transpose(
numpy.array([
in_vecs[0].GetTuple(k_tuple), in_vecs[1].GetTuple(k_tuple),
in_vecs[2].GetTuple(k_tuple)
]))
if (R is None):
R = numpy.eye(3)
if (out_vecs is None):
out_R = numpy.eye(3)
else:
out_R = numpy.transpose(
numpy.array([
out_vecs[0].GetTuple(k_tuple),
out_vecs[1].GetTuple(k_tuple),
out_vecs[2].GetTuple(k_tuple)
]))
full_R = numpy.dot(numpy.dot(numpy.transpose(in_R), R), out_R)
new_vector[:] = numpy.dot(numpy.transpose(full_R), old_vector)
new_array.SetTuple(k_tuple, new_vector)
return new_array
def moveMeshWithWorldMatrix(mesh, M, verbose=0):
mypy.my_print(verbose, "*** moveMeshWithWorldMatrix ***")
n_points = mesh.GetNumberOfPoints()
points = mesh.GetPoints()
P = numpy.empty(4)
for k_point in xrange(n_points):
P[0:3] = points.GetPoint(k_point)
P[3] = 1.
#print P
P = numpy.dot(M, P)
#print new_P
points.SetPoint(k_point, P[0:3])
def getClippedPDataUsingPlane(
pdata_mesh,
plane_O,
plane_N,
generate_clipped_output=False, # 2017/12/01: this seems to mess up everything with the returned pointers…
verbose=0):
mypy.my_print(verbose, "*** getClippedPDataUsingPlane ***")
plane = vtk.vtkPlane()
plane.SetOrigin(plane_O)
plane.SetNormal(plane_N)
#mypy.my_print(verbose-1, "pdata_mesh.GetBounds() = "+str(pdata_mesh.GetBounds()))
#mypy.my_print(verbose-1, "plane_O = "+str(plane_O))
#mypy.my_print(verbose-1, "plane_N = "+str(plane_N))
clip = vtk.vtkClipPolyData()
clip.SetClipFunction(plane)
if (generate_clipped_output):
clip.GenerateClippedOutputOn()
if (vtk.vtkVersion.GetVTKMajorVersion() >= 6):
clip.SetInputData(pdata_mesh)
else:
clip.SetInput(pdata_mesh)
clip.Update()
if (generate_clipped_output):
clipped0 = clip.GetOutput(0)
clipped1 = clip.GetOutput(1)
else:
clipped = clip.GetOutput()
#mypy.my_print(verbose-1, "clipped0.GetNumberOfPoints() = "+str(clipped0.GetNumberOfPoints()))
#mypy.my_print(verbose-1, "clipped1.GetNumberOfPoints() = "+str(clipped1.GetNumberOfPoints()))
#mypy.my_print(verbose-1, "clipped0.GetNumberOfCells() = "+str(clipped0.GetNumberOfCells()))
#mypy.my_print(verbose-1, "clipped1.GetNumberOfCells() = "+str(clipped1.GetNumberOfCells()))
#if (myvtk.getPDataSurfaceArea(clipped0) >= myvtk.getPDataSurfaceArea(clipped1)):
#return clipped0, clipped1
#else:
#return clipped1, clipped0
if (generate_clipped_output):
return clipped0, clipped1
else:
return clipped
def addVertices(ugrid, verbose=0):
mypy.my_print(verbose, "*** addVertices ***")
cell = vtk.vtkVertex()
cell_array = vtk.vtkCellArray()
n_points = ugrid.GetPoints().GetNumberOfPoints()
for k_point in xrange(n_points):
cell.GetPointIds().SetId(0, k_point)
cell_array.InsertNextCell(cell)
ugrid.SetCells(vtk.VTK_VERTEX, cell_array)
n_arrays = ugrid.GetPointData().GetNumberOfArrays()
for k_array in xrange(n_arrays):
ugrid.GetCellData().AddArray(ugrid.GetPointData().GetArray(k_array))
def addPDataNormals(
pdata,
orient_outward=1,
verbose=0):
mypy.my_print(verbose, "*** addPDataNormals ***")
pdata_normals = vtk.vtkPolyDataNormals()
pdata_normals.ComputePointNormalsOff()
pdata_normals.ComputeCellNormalsOn()
if (vtk.vtkVersion.GetVTKMajorVersion() >= 6):
pdata_normals.SetInputData(pdata)
else:
pdata_normals.SetInput(pdata)
pdata_normals.Update()
pdata.GetCellData().SetNormals(pdata_normals.GetOutput().GetCellData().GetNormals())
if (orient_outward):
cell_centers = myvtk.getCellCenters(
mesh=pdata,
verbose=verbose-1)
cell_center = numpy.empty(3)
mesh_center = numpy.array(pdata.GetCenter())
normals = pdata.GetCellData().GetNormals()
normal = numpy.empty(3)
cnt_pos = 0
cnt_neg = 0
for k_cell in xrange(pdata.GetNumberOfCells()):
cell_centers.GetPoint(k_cell, cell_center)
outward = cell_center-mesh_center
outward /= numpy.linalg.norm(outward)
normals.GetTuple(k_cell, normal)
proj = numpy.dot(outward, normal)
if (proj > 0): cnt_pos += 1
else: cnt_neg += 1
#print cnt_pos
#print cnt_neg
if (cnt_neg > cnt_pos):
pdata_normals.FlipNormalsOn()
pdata_normals.Update()
pdata.GetCellData().SetNormals(pdata_normals.GetOutput().GetCellData().GetNormals())
def addStrainsFromDisplacements(mesh,
disp_array_name="Displacement",
defo_grad_array_name="DeformationGradient",
strain_array_name="Strain",
mesh_w_local_basis=None,
verbose=0):
mypy.my_print(verbose, "*** addStrainsFromDisplacements ***")
myvtk.addDeformationGradients(mesh=mesh,
disp_array_name=disp_array_name,
verbose=verbose - 1)
myvtk.addStrainsFromDeformationGradients(
mesh=mesh,
defo_grad_array_name=defo_grad_array_name,
strain_array_name=strain_array_name,
mesh_w_local_basis=mesh_w_local_basis,
verbose=verbose - 1)
def writePData(pdata, filename, verbose=0):
mypy.my_print(verbose, "*** writePData: " + filename + " ***")
if (filename.endswith("vtk")):
pdata_writer = vtk.vtkPolyDataWriter()
elif (filename.endswith("vtp")):
pdata_writer = vtk.vtkXMLPolyDataWriter()
else:
assert 0, "File must be .vtk or .vtp. Aborting."
pdata_writer.SetFileName(filename)
if (vtk.vtkVersion.GetVTKMajorVersion() >= 6):
pdata_writer.SetInputData(pdata)
else:
pdata_writer.SetInput(pdata)
pdata_writer.Update()
pdata_writer.Write()
def writeSGrid(sgrid, filename, verbose=0):
mypy.my_print(verbose, "*** writeSGrid: " + filename + " ***")
if ('vtk' in filename):
sgrid_writer = vtk.vtkStructuredGridWriter()
elif ('vts' in filename):
sgrid_writer = vtk.vtkXMLStructuredGridWriter()
else:
assert 0, "File must be .vtk or .vts. Aborting."
sgrid_writer.SetFileName(filename)
if (vtk.vtkVersion.GetVTKMajorVersion() >= 6):
sgrid_writer.SetInputData(sgrid)
else:
sgrid_writer.SetInput(sgrid)
sgrid_writer.Update()
sgrid_writer.Write()
def getImageInterpolator(image, mode="linear", out_value=None, verbose=0):
mypy.my_print(verbose, "*** getImageInterpolator ***")
interpolator = vtk.vtkImageInterpolator()
assert (mode in ("nearest", "linear", "cubic"))
if (mode == "nearest"):
interpolator.SetInterpolationModeToNearest()
elif (mode == "linear"):
interpolator.SetInterpolationModeToLinear()
elif (mode == "cubic"):
interpolator.SetInterpolationModeToCubic()
if (out_value is not None):
interpolator.SetOutValue(out_value)
interpolator.Initialize(image)
interpolator.Update()
return interpolator
def getClippedPDataUsingField(pdata_mesh,
array_name,
threshold_value,
verbose=0):
mypy.my_print(verbose, "*** getClippedPDataUsingField ***")
pdata_mesh.GetPointData().SetActiveScalars(array_name)
clip_poly_data = vtk.vtkClipPolyData()
if (vtk.vtkVersion.GetVTKMajorVersion() >= 6):
clip_poly_data.SetInputData(pdata_mesh)
else:
clip_poly_data.SetInput(pdata_mesh)
clip_poly_data.SetValue(threshold_value)
clip_poly_data.GenerateClippedOutputOn()
clip_poly_data.Update()
return clip_poly_data.GetOutput(0), clip_poly_data.GetOutput(1)
def rotatePoints(
points,
C,
R,
verbose=0):
mypy.my_print(verbose, "*** rotatePoints ***")
n_points = points.GetNumberOfPoints()
point = numpy.empty(3)
for k_point in xrange(n_points):
points.GetPoint(k_point, point)
#print point
point = C + numpy.dot(R, point - C)
#print new_point
points.SetPoint(k_point, point)
def addVertices(
ugrid,
verbose=0):
mypy.my_print(verbose, "*** addVertices ***")
cell = vtk.vtkVertex()
cell_array = vtk.vtkCellArray()
n_points = ugrid.GetPoints().GetNumberOfPoints()
for k_point in xrange(n_points):
cell.GetPointIds().SetId(0, k_point)
cell_array.InsertNextCell(cell)
ugrid.SetCells(vtk.VTK_VERTEX, cell_array)
n_arrays = ugrid.GetPointData().GetNumberOfArrays()
for k_array in xrange(n_arrays):
ugrid.GetCellData().AddArray(ugrid.GetPointData().GetArray(k_array))
def moveMeshWithWorldMatrix(
mesh,
M,
verbose=0):
mypy.my_print(verbose, "*** moveMeshWithWorldMatrix ***")
n_points = mesh.GetNumberOfPoints()
points = mesh.GetPoints()
P = numpy.empty(4)
for k_point in xrange(n_points):
P[0:3] = points.GetPoint(k_point)
P[3] = 1.
#print P
P = numpy.dot(M, P)
#print new_P
points.SetPoint(k_point, P[0:3])
def getThresholdedPData(
pdata,
field_support,
field_name,
threshold_value,
threshold_by_upper_or_lower,
verbose=0):
mypy.my_print(verbose, "*** getThresholdedPData ***")
thresholded_ugrid = getThresholdedUGrid(
pdata,
field_support,
field_name,
threshold_value,
threshold_by_upper_or_lower,
False)
thresholded_pdata = ugrid2pdata(thresholded_ugrid, False)
return thresholded_pdata
def writeUGrid(
ugrid,
filename,
verbose=0):
mypy.my_print(verbose, "*** writeUGrid: "+filename+" ***")
if ('vtk' in filename):
ugrid_writer = vtk.vtkUnstructuredGridWriter()
elif ('vtu' in filename):
ugrid_writer = vtk.vtkXMLUnstructuredGridWriter()
else:
assert 0, "File must be .vtk or .vtu. Aborting."
ugrid_writer.SetFileName(filename)
if (vtk.vtkVersion.GetVTKMajorVersion() >= 6):
ugrid_writer.SetInputData(ugrid)
else:
ugrid_writer.SetInput(ugrid)
ugrid_writer.Update()
ugrid_writer.Write()
def writePData(
pdata,
filename,
verbose=0):
mypy.my_print(verbose, "*** writePData: "+filename+" ***")
if ('vtk' in filename):
pdata_writer = vtk.vtkPolyDataWriter()
elif ('vtp' in filename):
pdata_writer = vtk.vtkXMLPolyDataWriter()
else:
assert 0, "File must be .vtk or .vtp. Aborting."
pdata_writer.SetFileName(filename)
if (vtk.vtkVersion.GetVTKMajorVersion() >= 6):
pdata_writer.SetInputData(pdata)
else:
pdata_writer.SetInput(pdata)
pdata_writer.Update()
pdata_writer.Write()
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 readImage(
filename,
verbose=0):
mypy.my_print(verbose, "*** readImage: "+filename+" ***")
assert (os.path.isfile(filename)), "Wrong filename (\""+filename+"\"). Aborting."
if ('vtk' in filename):
image_reader = vtk.vtkImageDataReader()
elif ('vti' in filename):
image_reader = vtk.vtkXMLImageDataReader()
else:
assert 0, "File must be .vtk or .vti. Aborting."
image_reader.SetFileName(filename)
image_reader.Update()
image = image_reader.GetOutput()
mypy.my_print(verbose-1, "n_points = "+str(image.GetNumberOfPoints()))
return image
def getImageDimensionality(image, verbose=0):
mypy.my_print(verbose, "*** getImageDimensionality ***")
extent = image.GetExtent()
DX = extent[1] + 1 - extent[0]
DY = extent[3] + 1 - extent[2]
DZ = extent[5] + 1 - extent[4]
if (DX > 1) and (DY > 1) and (DZ > 1):
dimensionality = 3
elif (DX > 1) and (DY > 1) and (DZ == 1):
dimensionality = 2
elif (DX > 1) and (DY == 1) and (DZ == 1):
dimensionality = 1
else:
assert 0, "Wrong image dimensionality (" + str(extent) + ")"
# dimensionality = sum([extent[2*k_dim+1]>extent[2*k_dim] for k_dim in range(3)])
mypy.my_print(verbose - 1, "dimensionality = " + str(dimensionality))
return dimensionality
def getCellLocator(
mesh,
verbose=0):
mypy.my_print(verbose, "*** getCellLocator ***")
cell_locator = vtk.vtkCellLocator()
cell_locator.SetDataSet(mesh)
cell_locator.Update()
closest_point = [0.]*3
generic_cell = vtk.vtkGenericCell()
k_cell = vtk.mutable(0)
subId = vtk.mutable(0)
dist = vtk.mutable(0.)
return (cell_locator,
closest_point,
generic_cell,
k_cell,
subId,
dist)
def getImageInterpolator(
image,
mode="linear",
out_value=None,
verbose=0):
mypy.my_print(verbose, "*** getImageInterpolator ***")
interpolator = vtk.vtkImageInterpolator()
assert (mode in ("nearest", "linear", "cubic"))
if (mode == "nearest"):
interpolator.SetInterpolationModeToNearest()
elif (mode == "linear"):
interpolator.SetInterpolationModeToLinear()
elif (mode == "cubic"):
interpolator.SetInterpolationModeToCubic()
if (out_value is not None):
interpolator.SetOutValue(out_value)
interpolator.Initialize(image)
interpolator.Update()
return interpolator
def writeImage(
image,
filename,
verbose=0):
mypy.my_print(verbose, "*** writeImage: "+filename+" ***")
if ('vtk' in filename):
image_writer = vtk.vtkImageWriter()
elif ('vti' in filename):
image_writer = vtk.vtkXMLImageDataWriter()
else:
assert 0, "File must be .vtk or .vti. Aborting."
mypy.my_print(verbose, "n_points = "+str(image.GetNumberOfPoints()))
image_writer.SetFileName(filename)
if (vtk.vtkVersion.GetVTKMajorVersion() >= 6):
image_writer.SetInputData(image)
else:
image_writer.SetInput(image)
image_writer.Update()
image_writer.Write()
def getPointsInCell(
points,
cell,
verbose=0):
mypy.my_print(verbose, "*** getPointsInCell ***")
ugrid_cell = vtk.vtkUnstructuredGrid()
ugrid_cell.SetPoints(cell.GetPoints())
cell = vtk.vtkHexahedron()
for k_point in xrange(8): cell.GetPointIds().SetId(k_point, k_point)
cell_array_cell = vtk.vtkCellArray()
cell_array_cell.InsertNextCell(cell)
ugrid_cell.SetCells(vtk.VTK_HEXAHEDRON, cell_array_cell)
geometry_filter = vtk.vtkGeometryFilter()
if (vtk.vtkVersion.GetVTKMajorVersion() >= 6):
geometry_filter.SetInputData(ugrid_cell)
else:
geometry_filter.SetInput(ugrid_cell)
geometry_filter.Update()
cell_boundary = geometry_filter.GetOutput()
pdata_points = vtk.vtkPolyData()
pdata_points.SetPoints(points)
enclosed_points_filter = vtk.vtkSelectEnclosedPoints()
enclosed_points_filter.SetSurfaceData(cell_boundary)
if (vtk.vtkVersion.GetVTKMajorVersion() >= 6):
enclosed_points_filter.SetInputData(pdata_points)
else:
enclosed_points_filter.SetInput(pdata_points)
enclosed_points_filter.Update()
points_in_cell = [k_point for k_point in xrange(points.GetNumberOfPoints()) if enclosed_points_filter.GetOutput().GetPointData().GetArray('SelectedPoints').GetTuple1(k_point)]
return points_in_cell
def addImageGradient(
image,
image_dimensionality=None,
verbose=0):
mypy.my_print(verbose, "*** addImageGradient ***")
if (image_dimensionality is None):
image_dimensionality = myvtk.getImageDimensionality(
image=image,
verbose=verbose-1)
image_gradient = vtk.vtkImageGradient()
if (vtk.vtkVersion.GetVTKMajorVersion() >= 6):
image_gradient.SetInputData(image)
else:
image_gradient.SetInput(image)
image_gradient.SetDimensionality(image_dimensionality)
image_gradient.Update()
image_w_grad = image_gradient.GetOutput()
name = image.GetPointData().GetScalars().GetName()
image.GetPointData().AddArray(image_w_gradient.GetPointData().GetArray(name+"Gradient"))
image.GetPointData().SetActiveScalars(name+"Gradient")
