def test_arr2cell_array(self):
"""Test Numeric array to vtkCellArray conversion."""
# Test list of lists.
a = [[0], [1, 2], [3, 4, 5], [6, 7, 8, 9]]
cells = array_handler.array2vtkCellArray(a)
z = numpy.array([1, 0, 2, 1,2, 3, 3,4,5, 4, 6,7,8,9])
arr = array_handler.vtk2array(cells.GetData())
self.assertEqual(numpy.sum(arr - z), 0)
self.assertEqual(len(arr.shape), 1)
self.assertEqual(len(arr), 14)
# Test if optional argument stuff also works.
cells = vtk.vtkCellArray()
ident = id(cells)
cells = array_handler.array2vtkCellArray(a, cells)
self.assertEqual(id(cells), ident)
arr = array_handler.vtk2array(cells.GetData())
self.assertEqual(numpy.sum(arr - z), 0)
self.assertEqual(cells.GetNumberOfCells(), 4)
# Make sure this resets the cell array and does not add to the
# existing list!
cells = array_handler.array2vtkCellArray(a, cells)
self.assertEqual(cells.GetNumberOfCells(), 4)
# Test Numeric array handling.
N = 3
a = numpy.zeros((N,3), numpy.int)
a[:,1] = 1
a[:,2] = 2
cells = array_handler.array2vtkCellArray(a)
arr = array_handler.vtk2array(cells.GetData())
expect = numpy.array([3, 0, 1, 2]*3, numpy.int)
self.assertEqual(numpy.alltrue(numpy.equal(arr, expect)),
True)
self.assertEqual(cells.GetNumberOfCells(), N)
# Test if a list of Numeric arrays of different cell lengths works.
l_a = [a[:,:1], a, a[:2,:2]]
cells = array_handler.array2vtkCellArray(l_a)
arr = array_handler.vtk2array(cells.GetData())
expect = numpy.array([1, 0]*3 + [3, 0, 1, 2]*3 + [2, 0,1]*2, numpy.int)
self.assertEqual(numpy.alltrue(numpy.equal(arr, expect)),
True)
self.assertEqual(cells.GetNumberOfCells(), N*2 + 2)
# This should not take a long while. This merely tests if a
# million cells can be created rapidly.
N = int(1e6)
a = numpy.zeros((N,3), numpy.int)
a[:,1] = 1
a[:,2] = 2
cells = array_handler.array2vtkCellArray(a)
self.assertEqual(cells.GetNumberOfCells(), N)
def test_arr2cell_array(self):
"""Test Numeric array to vtkCellArray conversion."""
# Test list of lists.
a = [[0], [1, 2], [3, 4, 5], [6, 7, 8, 9]]
cells = array_handler.array2vtkCellArray(a)
z = numpy.array([1, 0, 2, 1, 2, 3, 3, 4, 5, 4, 6, 7, 8, 9])
arr = array_handler.vtk2array(cells.GetData())
self.assertEqual(numpy.sum(arr - z), 0)
self.assertEqual(len(arr.shape), 1)
self.assertEqual(len(arr), 14)
# Test if optional argument stuff also works.
cells = vtk.vtkCellArray()
ident = id(cells)
cells = array_handler.array2vtkCellArray(a, cells)
self.assertEqual(id(cells), ident)
arr = array_handler.vtk2array(cells.GetData())
self.assertEqual(numpy.sum(arr - z), 0)
self.assertEqual(cells.GetNumberOfCells(), 4)
# Make sure this resets the cell array and does not add to the
# existing list!
cells = array_handler.array2vtkCellArray(a, cells)
self.assertEqual(cells.GetNumberOfCells(), 4)
# Test Numeric array handling.
N = 3
a = numpy.zeros((N, 3), numpy.int)
a[:, 1] = 1
a[:, 2] = 2
cells = array_handler.array2vtkCellArray(a)
arr = array_handler.vtk2array(cells.GetData())
expect = numpy.array([3, 0, 1, 2] * 3, numpy.int)
self.assertEqual(numpy.alltrue(numpy.equal(arr, expect)), True)
self.assertEqual(cells.GetNumberOfCells(), N)
# Test if a list of Numeric arrays of different cell lengths works.
l_a = [a[:, :1], a, a[:2, :2]]
cells = array_handler.array2vtkCellArray(l_a)
arr = array_handler.vtk2array(cells.GetData())
expect = numpy.array([1, 0] * 3 + [3, 0, 1, 2] * 3 + [2, 0, 1] * 2,
numpy.int)
self.assertEqual(numpy.alltrue(numpy.equal(arr, expect)), True)
self.assertEqual(cells.GetNumberOfCells(), N * 2 + 2)
# This should not take a long while. This merely tests if a
# million cells can be created rapidly.
N = int(1e6)
a = numpy.zeros((N, 3), numpy.int)
a[:, 1] = 1
a[:, 2] = 2
cells = array_handler.array2vtkCellArray(a)
self.assertEqual(cells.GetNumberOfCells(), N)
def dolfin2polydata(mesh):
"""Convert dolfin mesh to vtk polydata
:param mesh: dolfin mesh
:returns: mesh in vtk polydata format
:rtype: vtk.vtkPolyData
"""
import vtk
from tvtk.array_handler import array2vtkPoints, array2vtkCellArray
gdim = mesh.geometry().dim()
mdim = mesh.topology().dim()
order = 1
# coordinates
pts = array2vtkPoints(mesh.coordinates())
# connectivity
dim = mesh.topology().dim()
ndof = dolfin.Cell(mesh, 0).num_vertices()
conn = mesh.topology()(dim, 0)().reshape((-1, ndof))
elms = array2vtkCellArray(conn)
grid = vtk.vtkPolyData()
grid.SetPoints(pts)
# only these are supported by dolfin
vtk_shape = {
1: {
1: vtk.VTK_LINE,
2: vtk.VTK_TRIANGLE,
3: vtk.VTK_TETRA
},
2: {
1: vtk.VTK_QUADRATIC_EDGE,
2: vtk.VTK_QUADRATIC_TRIANGLE,
3: vtk.VTK_QUADRATIC_TETRA,
},
}[1][mdim]
grid.SetLines(elms)
return grid
def dolfin2vtu(mesh):
"""Convert dolfin mesh to vtk unstructured grid
:param mesh: dolfin mesh
:returns: mesh in vtk unstructured grid format
:rtype: vtk.vtkUnstructuredGrid
"""
import vtk
domain = mesh.ufl_domain()
gdim = domain.geometric_dimension()
mdim = domain.topological_dimension()
order = 1
# coordinates of the mesh
coords = mesh.coordinates().copy()
# connectivity
conn = mesh.cells()
coords = np.hstack([coords, np.zeros((coords.shape[0], 3 - gdim))])
# only these are supported by dolfin
vtk_shape = {
1: {
1: vtk.VTK_LINE,
2: vtk.VTK_TRIANGLE,
3: vtk.VTK_TETRA
},
2: {
1: vtk.VTK_QUADRATIC_EDGE,
2: vtk.VTK_QUADRATIC_TRIANGLE,
3: vtk.VTK_QUADRATIC_TETRA,
},
}[order][mdim]
# create the grid
from tvtk.array_handler import array2vtkPoints, array2vtkCellArray
grid = vtk.vtkUnstructuredGrid()
grid.SetPoints(array2vtkPoints(coords))
grid.SetCells(vtk_shape, array2vtkCellArray(conn))
return grid