def exportVtk(self, filename):
"""Method for exporting fem calculation output to VTK-compatible format"""
print("Exporting results to '%s'..." % filename)
# --- Create points and polygon definitions from our node network
points = self.outputData.coords.tolist()
# --- Make sure topology is VTK-compatible; i.e.: 0-based
#polygons = (self.outputData.edof-1).tolist()
topo = np.zeros([self.outputData.edof.shape[0], 3], dtype=int)
for i in range(self.outputData.edof.shape[0]):
topo[i, 0] = self.outputData.edof[i, 1] / 2 - 1
topo[i, 1] = self.outputData.edof[i, 3] / 2 - 1
topo[i, 2] = self.outputData.edof[i, 5] / 2 - 1
polygons = (topo).tolist()
# --- Specify both vector and scalar data for each element
#pointData = vtk.PointData(vtk.Scalars(self.outputData.a.tolist(), name="Displacement"))
#cellData = vtk.CellData(vtk.Scalars(max(self.outputData.stress), name="maxvmstress"),\
# vtk.Vectors(self.outputData.stress, "stress"))
cellData = vtk.CellData(
vtk.Scalars(self.outputData.stress, name="Von Mises"))
# --- Create the structure of the element network
structure = vtk.PolyData(points=points, polygons=polygons)
# --- Store everything in a vtk instance
#vtkData = vtk.VtkData(structure, pointData, cellData)
vtkData = vtk.VtkData(structure, cellData)
# --- Save the data to the specified file
vtkData.tofile(filename, "ascii")
def _convert_species(self, species):
"""
Convert the given species from the openPMD format to a VTK container.
Parameters
----------
species: str
Name of the specis
ex. : 'electrons', 'He+1'
Returns
-------
pts_vtk: vtk.PolyData
VTK PolyData container with the particles 3D positions
scalars_vtk: list of vtk.Scalars
List of scalars associated with the particles
"""
# Get the particle data
pts = self.ts.get_particle(var_list=['x', 'y', 'z']+self.scalars,
species=species, iteration=self.iteration,
select=self.select)
# Split coordinates and scalars
coords = np.array(pts[:3]).astype(self.dtype).T
scalars_to_add = pts[3:]
# Convert microns to meters
# Note: in further release of openPMD-viewer, coords
# are expected to be meters by default
coords *= 1e-6
# If zmin_fixed mode is chosen, shift the z-coordinates
# to match the fields box
if self.zmin_fixed is not None:
if self.zmin_orig is None:
print('zmin_fixed mode can only be use after the fields')
else:
coords[:,2] -= self.zmin_orig - self.zmin_fixed
# Create the points container
pts_vtk = vtk.PolyData(coords)
# Create the scalars containers
scalars_vtk = []
for i, scalar in enumerate(scalars_to_add):
scalars_vtk.append(vtk.Scalars(scalar.astype(self.dtype),
name=self.scalars[i]))
return pts_vtk, scalars_vtk
def exportVtk(self, filename):
"""Export results to VTK"""
print("Exporting results to %s." % filename)
# --- Skapa punkter och polygon definitioner från vårt nät
points = self.outputData.coords.tolist()
# --- Tänk på att topologin i VTK är 0-baserad varför vi måste minskar **edof** med 1.
#polygons = (self.outputData.edof-1).tolist()
# --- För spänningsproblemet användas, se också nästa stycke:
polygons = (self.outputData.topo - 1).tolist()
# --- Resultat från beräkningen skapas i separata objekt. Punkter i vtk.PointData och
# --- elementdata i vtk.CellData. Nedan anger vi både vektor data och skalärvärden för elementen.
# --- Tänk på att vektorerna måste ha 3 komponenter, så lägg till detta i beräkningsdelen.
#pointData = vtk.PointData(vtk.Scalars(self.outputData.a.tolist(), name="Nodal Properties"))
#ellData = vtk.CellData(vtk.Scalars(self.outputData.vonMises, name="Von Mises"), vtk.Vectors(self.outputData.flow, "flow"))
# --- För spänningsproblemet blir det istället (ingen pointData)
#HÄR BLIR DET KNAS#
cellData = vtk.CellData(
vtk.Scalars(self.outputData.vonMises, name="mises"),
vtk.Vectors(self.outputData.stresses1, "principal stress 1"),
vtk.Vectors(self.outputData.stresses2, "principal stress 2"))
# --- Skapa strukturen för elementnätet.
structure = vtk.PolyData(points=points, polygons=polygons)
# --- Lagra allting i en vtk.VtkData instans
# vtkData = vtk.VtkData(structure, pointData, cellData)
# --- För spänningsfallet
vtkData = vtk.VtkData(structure, cellData)
# --- Spara allt till filen
vtkData.tofile(filename, "ascii")
def __init__(self, mesh, header="", directory=".", filename="unnamed"):
self.mesh = mesh
self.directory = directory
self.filename = filename
if isinstance(mesh, HexagonalMesh):
structure = pyvtk.PolyData(points=mesh.vertices,
polygons=mesh.hexagons)
elif isinstance(mesh, CuboidMesh):
# for keyword argument dimensions: if the mesh is made up of
# nx * ny * nz cells, it has (nx + 1) * (ny + 1) * (nz + 1)
# vertices.
structure = pyvtk.RectilinearGrid(*mesh.grid)
else:
raise NotImplementedError(
"Mesh should be CuboidMesh or HexagonalMesh, is {}.".format(
mesh.__class__.__name__))
self.structure = structure
self.header = header
self.init_VtkData(structure, header)
def off_mesh_file_to_vtk(input_filename,
output_filename,
data_format="binary",
coord_transform=None):
"""Convert a mesh file from OFF format to VTK format"""
print("Reading {}".format(input_filename))
with gzip.open(input_filename, "rt") as f:
header_keyword = f.readline().strip()
match = re.match(r"(ST)?(C)?(N)?(4)?(n)?OFF", header_keyword)
# TODO check features from header keyword
assert match
assert not match.group(5) # nOFF is unsupported
dimension_line = f.readline().strip()
match = re.match(r"([+-]?[0-9]+)\s+([+-]?[0-9]+)(\s+([+-]?[0-9]+))?",
dimension_line)
assert match
num_vertices = int(match.group(1))
num_triangles = int(match.group(2))
vertices = np.empty((num_vertices, 3), dtype=np.float)
for i in range(num_vertices):
components = f.readline().split()
assert len(components) >= 3
vertices[i, 0] = float(components[0])
vertices[i, 1] = float(components[1])
vertices[i, 2] = float(components[2])
triangles = np.empty((num_triangles, 3), dtype=np.int_)
for i in range(num_triangles):
components = f.readline().split()
assert len(components) >= 4
assert components[0] == "3"
triangles[i, 0] = float(components[1])
triangles[i, 1] = float(components[2])
triangles[i, 2] = float(components[3])
print()
print("{0} vertices and {1} triangles read".format(num_vertices,
num_triangles))
points = vertices
if coord_transform is not None:
if coord_transform.shape[0] == 4:
assert np.all(coord_transform[3, :] == [0, 0, 0, 1])
points = points.T
points = np.dot(coord_transform[:3, :3], points)
points += coord_transform[:3, 3, np.newaxis]
points = points.T
if np.linalg.det(coord_transform[:3, :3]) < 0:
# Flip the triangles to fix inside/outside
triangles = np.flip(triangles, axis=1)
# Gifti uses millimetres, Neuroglancer expects nanometres
points *= 1e6
# Workaround: dtype must be np.int_ (pyvtk does not recognize int32 as
# integers)
triangles = triangles.astype(np.int_)
vtk_mesh = pyvtk.PolyData(points, polygons=triangles)
vtk_data = pyvtk.VtkData(
vtk_mesh, "Converted using "
"https://github.com/HumanBrainProject/neuroglancer-scripts")
vtk_data.tofile(output_filename, format=data_format)
def export_vtk_stress(filename,
coords,
topo,
a=None,
el_scalar=None,
el_vec1=None,
el_vec2=None):
"""
Export mesh and results for a 2D stress problem.
Parameters:
filename Filename of vtk-file
coords Element coordinates (np.array)
topo Element topology (not dof topology). mesh.topo. (np.array)
a Element displacements 2-dof (np.array)
el_scalar Scalar values for each element (list)
el_vec1 Vector value for each element (list)
el_vec2 Vector value for each element (list)
"""
points = coords.tolist()
polygons = (topo - 1).tolist()
displ = []
point_data = None
scalars = None
vectors1 = None
vectors2 = None
cell_data = None
if a is not None:
for i in range(0, len(a), 2):
displ.append([np.asscalar(a[i]), np.asscalar(a[i + 1]), 0.0])
point_data = vtk.PointData(vtk.Vectors(displ, name="displacements"))
if el_scalar is not None:
scalars = vtk.Scalars(el_scalar, name="scalar")
if el_vec1 is not None:
vectors1 = vtk.Vectors(el_vec1, name="principal1")
if el_vec2 is not None:
vectors2 = vtk.Vectors(el_vec2, name="principal2")
if el_scalar is not None and el_vec1 is None and el_vec2 is None:
cell_data = vtk.CellData(scalars)
if el_scalar is not None and el_vec1 is None and el_vec2 is not None:
cell_data = vtk.CellData(scalars, vectors2)
if el_scalar is not None and el_vec1 is not None and el_vec2 is None:
cell_data = vtk.CellData(scalars, vectors1)
if el_scalar is not None and el_vec1 is not None and el_vec2 is None:
cell_data = vtk.CellData(scalars, vectors1, vectors2)
if el_scalar is None and el_vec1 is None and el_vec2 is not None:
cell_data = vtk.CellData(vectors2)
if el_scalar is None and el_vec1 is not None and el_vec2 is None:
cell_data = vtk.CellData(vectors1)
if el_scalar is None and el_vec1 is not None and el_vec2 is None:
cell_data = vtk.CellData(vectors1, vectors2)
structure = vtk.PolyData(points=points, polygons=polygons)
if cell_data is not None and point_data is not None:
vtk_data = vtk.VtkData(structure, cell_data, point_data)
if cell_data is None and point_data is not None:
vtk_data = vtk.VtkData(structure, point_data)
if cell_data is None and point_data is None:
vtk_data = vtk.VtkData(structure)
vtk_data.tofile("exm6.vtk", "ascii")
def write_species_vtk(self,
species=None,
iteration=0,
format='binary',
scalars=['ux', 'uy', 'uz', 'w'],
select=None,
zmin_fixed=None,
sample_ptcl=None):
"""
Convert the given list of species from the openPMD format to
a VTK container, and write it to the disk.
Parameters
----------
species: list or None
List of species names to be converted. If None, it
converts all available species provided by OpenPMDTimeSeries
scalars: list of strings
list of values associated with each paricle to be included.
ex. : 'charge', 'id', 'mass', 'x', 'y', 'z', 'ux', 'uy', 'uz', 'w'
iteration: int
iteration number to treat (default 0)
select: dict
dictonary to impoer selection on the particles,
as it is defined in opnePMD_viewer
format: str
format for the VTK file, either 'ascii' or 'binary'
zmin_fixed: float or None
When treating the simulation data for the animation, in
some cases (e.g. with moving window) it is useful to
fix the origin of the visualization domain. If float number
is given it will be use as z-origin of the visualization domain
sample_ptcl: integer or None
If not None, the species arrays will be reduced by skipping
elements
"""
# Check available fields if comps is not defined
if species is None:
species = self.ts.avail_species
# register constants
self.iteration = iteration
self.zmin_fixed = zmin_fixed
self.select = select
self.scalars = scalars
if sample_ptcl is None:
self.sample_ptcl = 1
else:
self.sample_ptcl = sample_ptcl
# Make a numer string for the file to write
istr = str(self.iteration)
while len(istr) < 7:
istr = '0' + istr
name_base = self.path + 'vtk_specie_{:}_{:}'
# Convert and save all the species
for specie in species:
points, scalars_to_add = self._get_species(specie)
# Create the points container
pts_vtk = vtk.PolyData(points)
# Create the scalars containers
scalars_vtk = []
for i, scalar in enumerate(scalars_to_add):
scalars_vtk.append(vtk.Scalars(scalar, name=self.scalars[i]))
vtk.VtkData(pts_vtk, vtk.PointData(*scalars_vtk) )\
.tofile(name_base.format(specie,istr), format=format)
import sys
sys.path = ['..'] + sys.path
#from pyvtk import *
import pyvtk as vtk
structure = vtk.PolyData(points=[[0, 0, 0], [1, 0, 0], [1, 1, 0], [0, 1, 0],
[0, 0, 1], [1, 0, 1], [1, 1, 1], [0, 1, 1]],
polygons=[[0, 1, 2, 3], [4, 5, 6, 7], [0, 1, 5, 4],
[2, 3, 7, 6], [0, 4, 7, 3], [1, 2, 6, 5]])
pointdata = vtk.PointData(
vtk.Scalars([0, 1, 2, 3, 4, 5, 6, 7],
name='sample_scalars',
lookup_table='my_table'),
vtk.LookupTable([[0, 0, 0, 1], [1, 0, 0, 1], [0, 1, 0, 1], [1, 1, 0, 1],
[0, 0, 1, 1], [1, 0, 1, 1], [0, 1, 1, 1], [1, 1, 1, 1]],
name='my_table'))
celldata = vtk.CellData(
vtk.Scalars([0, 1, 2, 3, 4, 5], name='cell_scalars'),
vtk.Normals(
[[0, 0, -1], [0, 0, 1], [0, -1, 0], [0, 1, 0], [-1, 0, 0], [1, 0, 0]],
name='cell_normals'),
vtk.Field('FieldData',
cellIds=[[0], [1], [2], [3], [4], [5]],
faceAttributes=[[0, 1], [1, 2], [2, 3], [3, 4], [4, 5], [5, 6]]))
vtkdata = vtk.VtkData(structure, pointdata, celldata)
vtkdata.tofile('example1ascii', 'ascii')
#vtkdata.tofile('example1binary','binary')