def save_vtk(self, modei, scale):
path = str(
QFileDialog.getExistingDirectory(self,
"Select Directory")) + '/'
print path
U = self.MODOS.coord.copy()
nnos = self.MODOS.nnos
ngl = self.MODOS.ngl
nodesr = self.MODOS.nodesr
nodesl = list(set(range(nnos)) - set(nodesr))
scale = float(scale)
modei = int(modei) - 1
g = self.MODOS.g
U_i = zeros((nnos, g), float)
U_i[nodesl] = self.MODOS.modo[:, modei].reshape(
self.MODOS.modo[:, modei].size / g, g)
Ux, Uy, Uz = U_i[:, 0].copy(), U_i[:, 1].copy(), U_i[:, 2].copy()
U_i = U_i * scale
U = U + U_i[:, :3]
connec_face = self.MODOS.connec_face
vtk = pyvtk.VtkData(
pyvtk.UnstructuredGrid(U, triangle=connec_face),
pyvtk.PointData(pyvtk.Scalars(Ux, name='Ux'),
pyvtk.Scalars(Uy, name='Uy'),
pyvtk.Scalars(Uz, name='Uz')))
vtk.tofile(path + 'MODAL_' + str(modei + 1))
def tovtk(self, N, filename):
"""Dump probes to VTK file."""
is_root = comm.Get_rank() == 0
z = self.array(N=N)
if is_root:
d = self.dims
d = (d[0], d[1], d[2]) if len(d) > 2 else (d[0], d[1], 1)
grid = pyvtk.StructuredGrid(d, self.create_dense_grid())
v = pyvtk.VtkData(grid, "Probe data. Evaluations = {}".format(self.probes.number_of_evaluations()))
if self.probes.value_size() == 1:
v.point_data.append(pyvtk.Scalars(z, name="Scalar", lookup_table='default'))
elif self.probes.value_size() == 3:
v.point_data.append(pyvtk.Vectors(z, name="Vector"))
elif self.probes.value_size() == 9: # StatisticsProbes
if N == 0:
num_evals = self.probes.number_of_evaluations()
v.point_data.append(pyvtk.Vectors(z[:, :3]/num_evals, name="UMEAN"))
rs = ["uu", "vv", "ww", "uv", "uw", "vw"]
for i in range(3, 9):
v.point_data.append(pyvtk.Scalars(z[:, i]/num_evals, name=rs[i-3], lookup_table='default'))
else: # Just dump latest snapshot
v.point_data.append(pyvtk.Vectors(z[:, :3], name="U"))
else:
raise TypeError("Only vector or scalar data supported for VTK")
v.tofile(filename)
def dump_vtk_grid(self, path: str):
self.set_sigma()
point_coords = np.zeros([self.n_nodes, 3])
point_coords += self.a.reshape([self.n_nodes, 3])
point_coords[:, 0] += self.x_0
point_coords[:, 1] += self.y_0
point_velocities = self.a_t.reshape([self.n_nodes, 3])
pd = pvtk.PointData(pvtk.Vectors(point_velocities, name='Velocity'))
pd.append(pvtk.Scalars(point_coords[:, 2], name='z'))
triangles = []
sigmas = []
for elem in self.elements:
triangles.append(list(elem.node_ind))
sigmas.append(elem.sigma)
cd = []
names = [
'sigma_xx', 'sigma_yy', 'sigma_zz', 'tau_xy', 'tau_yz', 'tau_xz'
]
sigmas = np.array(sigmas)
for i in range(6):
cd.append(pvtk.Scalars(sigmas[:, i], name=names[i]))
usg = pvtk.UnstructuredGrid(point_coords, triangle=triangles)
vtk = pvtk.VtkData(usg, pd)
for e in cd:
vtk.cell_data.append(e)
vtk.tofile(path, 'binary')
def visitPrint(self, k):
"""
Uses PyVTK to write out data in a VisIt Visualization Tool capable format.
"""
import pyvtk
uVel = pyvtk.Scalars(self.fluid.u().flatten(), name='u')
vVel = pyvtk.Scalars(self.fluid.v().flatten(), name='v')
totp = pyvtk.Scalars(self.fluid.p().flatten(), name='p')
celldat = pyvtk.PointData(uVel, vVel, totp)
grid = pyvtk.RectilinearGrid(self.domain.x, self.domain.y,
self.domain.z)
vtk = pyvtk.VtkData(grid, celldat)
vtk.tofile('data%i' % k)
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 numpy2vtkgrid_file(outfilename,
xmin,
xmax,
ymin,
ymax,
numpy_matrix,
zlevel=0.0,
vtk_format='ascii',
vtkfilecomment="Created with numpy2vtkgrid",
vtkdatacomment="Scalar field"):
assert len(numpy_matrix.shape) == 2,\
"data needs to be 2d, but shape is '%s'" % numpy_matrix.shape
nx, ny = numpy_matrix.shape
xpos = numpy.linspace(xmin, xmax, nx)
ypos = numpy.linspace(ymin, ymax, ny)
print "point set = %d*%d=%d" % (nx, ny, nx * ny)
vtk = pyvtk.VtkData(
pyvtk.RectilinearGrid(\
xpos.tolist(),ypos.tolist(),[zlevel]
),
vtkfilecomment,
pyvtk.PointData(
pyvtk.Scalars( numpy_matrix.flatten().tolist(),
vtkdatacomment )
),
format=vtk_format
)
vtk.tofile(outfilename, format=vtk_format)
def _convert_field_scl(self, fld):
"""
Convert the given scalar or vector fields from the
openPMD format to a VTK container.
Parameters
----------
fld: str
Scalar and vector fields to be converted
ex. : 'E', 'B', 'J', 'rho'
converts all available components provided by OpenPMDTimeSeries
Returns
-------
scl: vtk.Scalars
VTK scalar containter
"""
# Choose the get_field and make_grid finctions for the given geometry
if self.geom=='3dcartesian':
get_field = self._get_opmd_field_3d
make_mesh = self._make_vtk_mesh_3d
elif self.geom=='thetaMode':
get_field = self._get_opmd_field_circ
make_mesh = self._make_vtk_mesh_circ
fld_data, self.info = get_field(fld)
make_mesh()
scl = vtk.Scalars(fld_data, name=fld)
return scl
def omf2vtk(input_omf_file,
output_vtk_file,
output_format='ascii'
):
"""
Convert a given input_omf_file into a VTK file in ascii or binary format
Magnetisation (direction and magnitude) values are stored as cell values
"""
data = MagnetisationData(input_omf_file)
data.generate_field()
data.generate_coordinates()
grid = (np.linspace(data.xmin * 1e9, data.xmax * 1e9, data.nx + 1),
np.linspace(data.ymin * 1e9, data.ymax * 1e9, data.ny + 1),
np.linspace(data.zmin * 1e9, data.zmax * 1e9, data.nz + 1))
structure = pyvtk.RectilinearGrid(* grid)
vtk_data = pyvtk.VtkData(structure, "")
# Save the magnetisation
vtk_data.cell_data.append(pyvtk.Vectors(np.column_stack((data.field_x,
data.field_y,
data.field_z)),
"m"))
# Save Ms as scalar field
vtk_data.cell_data.append(pyvtk.Scalars(data.field_norm, "Ms"))
# Save to VTK file with specified output filename
vtk_data.tofile(output_vtk_file, output_format)
def _vtk_addPointdata(vtk, data, name):
"""vtk is a vtk object (from pyvtk) to which the data will be appended.
data is a list of lists. The inner lists contain the data, the outer lists the sites.
Example: data = [[0.1],[0.2],[0.3],....] is scalar data
data = [[0.1,1],[0.2,0.5],[0.3,0.4],....] is 2d vector data
name is the name of the data (used in vtk file to label the field)"""
log.debug("Adding dof %s to vtk object" % name)
if type(data[0]) in [types.FloatType, types.IntType]:
#raw data in scalar data set, convert float a into [a]:
data = map(lambda a: [a], data)
#print "In vtk_addPointdata. What is the structure of data?"
#from IPython.Shell import IPShellEmbed
#ipshell = IPShellEmbed()
#ipshell()
if len(data[0]) == 1:
vtk.point_data.append(
pyvtk.Scalars(data, name=name, lookup_table='default'))
elif len(data[0]) in [2, 3]:
if len(data[0]) == 2:
#make 3d
data = map(lambda a: a + [0.], data)
vtk.point_data.append(pyvtk.Vectors(data, name=name))
else:
raise NfemValueError, "Can only deal with scalar or vector data"
return vtk
def test_tet_mesh(visualize=False):
pytest.importorskip("meshpy")
from math import pi, cos, sin
from meshpy.tet import MeshInfo, build
from meshpy.geometry import \
GeometryBuilder, generate_surface_of_revolution, EXT_CLOSED_IN_RZ
pytest.importorskip("meshpy")
big_r = 3
little_r = 1.5
points = 50
dphi = 2 * pi / points
rz = np.array(
[[big_r + little_r * cos(i * dphi), little_r * sin(i * dphi)]
for i in range(points)])
geo = GeometryBuilder()
geo.add_geometry(*generate_surface_of_revolution(
rz, closure=EXT_CLOSED_IN_RZ, radial_subdiv=20))
mesh_info = MeshInfo()
geo.set(mesh_info)
mesh = build(mesh_info)
def tet_face_vertices(vertices):
return [
(vertices[0], vertices[1], vertices[2]),
(vertices[0], vertices[1], vertices[3]),
(vertices[0], vertices[2], vertices[3]),
(vertices[1], vertices[2], vertices[3]),
]
face_map = {}
for el_id, el in enumerate(mesh.elements):
for fid, face_vertices in enumerate(tet_face_vertices(el)):
face_map.setdefault(frozenset(face_vertices), []).append(
(el_id, fid))
adjacency = {}
for face_vertices, els_faces in face_map.items():
if len(els_faces) == 2:
(e1, f1), (e2, f2) = els_faces
adjacency.setdefault(e1, []).append(e2)
adjacency.setdefault(e2, []).append(e1)
cuts, part_vert = pymetis.part_graph(17, adjacency)
if visualize:
import pyvtk
vtkelements = pyvtk.VtkData(
pyvtk.UnstructuredGrid(mesh.points, tetra=mesh.elements), "Mesh",
pyvtk.CellData(pyvtk.Scalars(part_vert, name="partition")))
vtkelements.tofile('split.vtk')
def writeVTK(self, filename):
import pyvtk
origin = N.array([self.x_axis[0], self.y_axis[0], self.z_axis[0]])
spacing = N.array([self.x_axis[1], self.y_axis[1], self.z_axis[1]]) \
- origin
values = pyvtk.Scalars(N.ravel(N.transpose(self.data)),
'electron density')
data = pyvtk.VtkData(
pyvtk.StructuredPoints(self.data.shape, origin, spacing),
'Density map', pyvtk.PointData(values))
data.tofile(filename, format='binary')
def test_vtk_writer_speed():
"""
Comparison of C backend with the old pyvtk interface
For this we use a 200 x 200 x 1 mesh and convert the OMF file into a VTK
file using both the C library and the PyVTK library. We run the same
conversion for each method during 20 times and print a mean.
"""
# C backend ---------------------------------------------------------------
_file = glob.glob('./vtk_writer_omfs/isolated_sk_Cnv_n_200-Oxs*.omf')[0]
data = op.MagnetisationData(_file)
data.generate_field()
data.generate_coordinates()
output_vtk_file = 'vtk_writer_omfs/isolated_sk_Cnv_n_200.vtk'
C_timings = []
for i in range(20):
start = timeit.default_timer()
ot.clib.WriteVTK_RectilinearGrid_C(data.grid[0],
data.grid[1], data.grid[2],
data.field.reshape(-1),
data.field_norm, data.nx, data.ny,
data.nz, output_vtk_file)
end = timeit.default_timer()
C_timings.append(end - start)
print('C writer (best of 20): ', np.mean(np.array(C_timings)))
# PyVTK -------------------------------------------------------------------
output_vtk_file = 'vtk_writer_omfs/isolated_sk_Cnv_n_200_pyvtk.vtk'
pyvtk_timings = []
for i in range(20):
start = timeit.default_timer()
structure = pyvtk.RectilinearGrid(*data.grid)
vtk_data = pyvtk.VtkData(structure, "")
# Save the magnetisation
vtk_data.cell_data.append(pyvtk.Vectors(data.field, "m"))
# Save Ms as scalar field
vtk_data.cell_data.append(pyvtk.Scalars(data.field_norm, "Ms"))
# Save to VTK file with specified output filename
vtk_data.tofile(output_vtk_file, 'binary')
end = timeit.default_timer()
pyvtk_timings.append(end - start)
print('PyVTK writer (best of 20): ', np.mean(np.array(pyvtk_timings)))
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 savevtk(v, fn='', lons=[], lats=[], levels=[]):
"""save tracer field into vtk format,
"""
import pyvtk
def norm(c):
return (c - c[0]) / (c[-1] - c[0])
z = levels / abs(levels).max() * (lons.max() - lons.min()) * 0.7
point_data = pyvtk.PointData(pyvtk.Scalars(v.T.flatten()))
vtk_object = pyvtk.VtkData(pyvtk.RectilinearGrid(x=lons, y=lats, z=z),
point_data)
vtk_object.tofile(fn)
return
def plot_vtk(A, V, partition) :
V = numpy.append( V, numpy.zeros((A.shape[0],1)), axis=1 )
triples = []
A = scipy.sparse.triu(A,k=1).tocsr()
for i in range(A.shape[0]-1):
row = A.indices[A.indptr[i]:A.indptr[i+1]].tolist()
for t1,t2 in itertools.combinations(row, 2) :
if A[t1,t2] :
triples.append((i,t1,t2))
vtkelements = pyvtk.VtkData(
pyvtk.UnstructuredGrid(V, triangle=triples),
"Mesh",
pyvtk.PointData(pyvtk.Scalars(partition, name="partition")))
vtkelements.tofile('{0}_{1}.vtk'.format(graph_name,num_parts))
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 _writevtk(self, filename):
grid = [
pmini + np.linspace(0, li, ni + 1)
for pmini, li, ni in zip(self.mesh.pmin, self.mesh.l, self.mesh.n)
]
structure = pyvtk.RectilinearGrid(*grid)
vtkdata = pyvtk.VtkData(structure)
vectors = [self.__call__(i) for i in self.mesh.coordinates]
vtkdata.cell_data.append(pyvtk.Vectors(vectors, self.name))
for i, component in enumerate(dfu.axesdict.keys()):
name = "{}_{}".format(self.name, component)
vtkdata.cell_data.append(
pyvtk.Scalars(list(zip(*vectors))[i], name))
vtkdata.tofile(filename)
def _convert_field(self, comp, iteration):
"""
Convert the given scalar or vector fields from the
openPMD format to a VTK container.
Parameters
----------
comp: str
Scalar and vector fields to be converted
ex. : 'E', 'B', 'J', 'rho'
converts all available components provided by OpenPMDTimeSeries
iteration: int
iteration number to treat (default 0)
"""
# Choose the get_field and make_grid finctions for the given geometry
if self.geom == '3dcartesian':
get_field = self._get_opmd_field_3d
make_mesh = self._make_vtk_mesh_3d
# Converting the vector field
if self.ts.fields_metadata[comp]['type'] == 'vector':
coords = self.ts.fields_metadata[comp]['axis_labels']
flds = []
for coord in coords:
self.fld, self.info = get_field(comp, iteration, coord=coord)
flds.append(self.fld.astype(np.float32).T.ravel())
make_mesh()
return vtk.Vectors(np.array(flds).T, name=comp)
# Converting the scalar field
elif self.ts.fields_metadata[comp]['type'] == 'scalar':
self.fld, self.info = get_field(comp, iteration)
make_mesh()
return vtk.Scalars(self.fld.astype(np.float32).T.ravel(),
name=comp)
else:
print('Error')
return None
def export_paraview(self):
if self.export_paraview == 0:
self.vtk_points = [_v.coord for _v in self.vertices[1:]]
self.vtk_triangle = [[
_e.vertices[0].tag - 1, _e.vertices[1].tag - 1,
_e.vertices[2].tag - 1
] for _e in self.elements[1:] if _e.typ == 2]
pressure = [np.abs(_v.sol[3]) for _v in self.vertices[1:]]
# Bidouille pour que la tour et les lettres clignotent dans IAGS 20201
pressure_max = max(pressure)
light_on = self.export_paraview % 4
if light_on < 2:
tower_on = 0
else:
tower_on = 1
for _ent in self.fem_entities:
if _ent.dim == 2:
if _ent.mat.MEDIUM_TYPE == "eqf":
if _ent.mat.name == "tower":
for _elem in _ent.elements:
for _v in _elem.vertices:
_v.sol[3] = (1 +
(-1)**tower_on) * (pressure_max / 2.)
if _ent.mat.name == "letter":
for _elem in _ent.elements:
for _v in _elem.vertices:
_v.sol[3] = (1 + (-1)**
(tower_on + 1)) * (pressure_max / 2.)
pressure = [np.abs(_v.sol[3]) for _v in self.vertices[1:]]
vtk = pyvtk.VtkData(
pyvtk.UnstructuredGrid(self.vtk_points, triangle=self.vtk_triangle),
pyvtk.PointData(pyvtk.Scalars(pressure, name='Pressure')))
vtk.tofile("vtk/" + self.name_project + "-{}".format(self.export_paraview))
self.export_paraview += 1
def loadVecToVTK(self, name, ndofs=1):
from petsc4py import PETSc
length = np.array(self._size).prod()
print 'loading', self._file_prefix + name
vec = PETSc.Vec().createSeq(length * ndofs)
viewer = PETSc.Viewer().createBinary(self._file_prefix + name,
PETSc.Viewer.Mode.R)
vec.load(viewer)
if self._size[2] == 1:
length = 2 * length
npvec = vec[...].reshape((self._size_r + (ndofs, )))[:]
npvec = np.repeat(npvec, 2, axis=0)
npvec = npvec.reshape((length, ndofs))
else:
npvec = vec[...].reshape((length, ndofs))[:]
# scale
if name.startswith('u'):
npvec = npvec * self._scalefactor
print np.where(np.abs(npvec) / np.abs(npvec).mean() > 1e2)[0]
npvec = np.where(
np.abs(npvec) / np.abs(npvec).mean() > 1e2, 0., npvec)
if ndofs == 1:
data = pyvtk.Scalars(npvec,
self._prefix.strip('_') + ' ' + name[:-7],
'default')
else:
data = pyvtk.Vectors([tuple(npvec[i, :]) for i in range(length)],
self._prefix.strip('_') + ' ' + name[:-7])
viewer.destroy()
vec.destroy()
del viewer
del vec
return data
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 _vtk_createVtkData(meshpoints,
meshsimplices,
data,
name,
header="Data header (unused)"):
#If data is list of float, convert into list of lists, each list containing one float
if type(data[0]) in [types.FloatType, types.IntType]:
#raw data in scalar data set, convert float a into [a]:
data = map(lambda a: [a], data)
#Due to inflexibility in pyvtk, we need to distinguish 4 different cases for
#2d-meshes with scalar data
#2d-meshes with vector data
#3d-meshes with scalar data
#3d-meshes with vector data
#Here we go:
if len(meshpoints[0]) == 2:
log.debug("Mesh seems 2d")
#make 3d for pyvtk
meshpoints = map(lambda pos: pos + [0.], meshpoints)
if len(data[0]) == 1:
log.debug("Data seems 1d (scalar)")
log.debug("Creating vtk data structure with dof '%s'" % name)
vtk = pyvtk.VtkData(
pyvtk.UnstructuredGrid(meshpoints, triangle=meshsimplices),
pyvtk.PointData(
pyvtk.Scalars(data, name=name, lookup_table='default')),
header)
elif len(data[0]) in [2, 3]:
if len(data[0]) == 2:
log.debug("Data seems 2d (vector)")
#make 3d for pyvtk
data = map(lambda a: a + [0.], data)
else:
log.debug("Data seems 3d (vector)")
log.debug("Creating vtk data structure with dof '%s'" % name)
vtk = pyvtk.VtkData(
pyvtk.UnstructuredGrid(meshpoints, triangle=meshsimplices),
pyvtk.PointData(pyvtk.Vectors(data, name=name)), header)
else:
raise NfemValueError, "Can only deal with scalar or vector data"
elif len(meshpoints[0]) == 3:
log.debug("Mesh seems 3d")
if len(data[0]) == 1:
log.debug("Data seems 1d (scalar)")
log.debug("Creating vtk data structure with dof '%s'" % name)
vtk = pyvtk.VtkData(
pyvtk.UnstructuredGrid(meshpoints, tetra=meshsimplices),
pyvtk.PointData(
pyvtk.Scalars(data, name=name, lookup_table='default')),
header)
elif len(data[0]) in [2, 3]:
if len(data[0]) == 2:
log.debug("Data seems 2d (vector)")
#make 3d for pyvtk
data = map(lambda a: a + [0.], data)
else:
log.debug("Data seems 3d (vector)")
log.debug("Creating vtk data structure with dof '%s'" % name)
vtk = pyvtk.VtkData(
pyvtk.UnstructuredGrid(meshpoints, tetra=meshsimplices),
pyvtk.PointData(pyvtk.Vectors(data, name=name)), header)
else:
raise NfemValueError, "Can only deal with scalar or vector data"
elif len(meshpoints[0]) == 1:
log.debug("Mesh seems 1d")
#make 3d for pyvtk
meshpoints = map(lambda pos: pos + [0., 0.], meshpoints)
if len(data[0]) == 1:
log.debug("Data seems 1d (scalar)")
log.debug("Creating vtk data structure with dof '%s'" % name)
vtk = pyvtk.VtkData(
pyvtk.UnstructuredGrid(meshpoints, line=meshsimplices),
pyvtk.PointData(
pyvtk.Scalars(data, name=name, lookup_table='default')),
header)
elif len(data[0]) in [2, 3]:
if len(data[0]) == 2:
log.debug("Data seems 2d (vector)")
#make 3d for pyvtk
data = map(lambda a: a + [0.], data)
else:
log.debug("Data seems 3d (vector)")
log.debug("Creating vtk data structure with dof '%s'" % name)
vtk = pyvtk.VtkData(
pyvtk.UnstructuredGrid(meshpoints, line=meshsimplices),
pyvtk.PointData(pyvtk.Vectors(data, name=name)), header)
else:
raise NfemValueError, "Can only deal with scalar or vector data"
else:
NfemValueError, "Mesh seems to be %d dimensional. Can only do 1, 2 or 3." % len(
meshpoints[0])
return vtk
def write_vtk(iproc):
if args.nproc == 1:
nc_surf_local = Dataset(args.in_surface_nc, 'r', format='NETCDF4')
iproc = 0
else:
# copy netcdf file for parallel access
tempnc = args.out_vtk + '/surface_temp.nc' + str(iproc)
shutil.copy(args.in_surface_nc, tempnc)
nc_surf_local = Dataset(tempnc, 'r', format='NETCDF4')
# write vtk
if args.verbose and iproc == 0:
clock0 = time.clock()
print('Generating snapshot...')
for it, istep in enumerate(steps):
if it % args.nproc != iproc:
continue
if args.min_step is not None:
if it < args.min_step:
continue
if args.max_step is not None:
if it > args.max_step:
continue
if args.norm:
disp_norm = np.zeros(nstation)
else:
disp = np.zeros((nstation, 3))
eleTag_last = -1
fourier_last = None
for istation, dist in enumerate(dists):
if eleTags[istation] == eleTag_last:
fourier = fourier_last
else:
fourier_r = nc_surf_local.variables['edge_' +
str(eleTags[istation]) +
'r'][istep, :]
fourier_i = nc_surf_local.variables['edge_' +
str(eleTags[istation]) +
'i'][istep, :]
fourier = fourier_r[:] + fourier_i[:] * 1j
fourier_last = fourier
eleTag_last = eleTags[istation]
nu_p_1 = int(len(fourier) / nPntEdge / 3)
wdotf = np.zeros((3, nu_p_1), dtype=fourier.dtype)
for idim in np.arange(0, 3):
start = idim * nPntEdge * nu_p_1
end = idim * nPntEdge * nu_p_1 + nPntEdge * nu_p_1
fmat = fourier[start:end].reshape(nPntEdge, nu_p_1)
wdotf[idim] = weights[istation].dot(fmat)
exparray = 2. * np.exp(np.arange(0, nu_p_1) * 1j * azims[istation])
exparray[0] = 1.
spz = wdotf.dot(exparray).real
if args.norm:
disp_norm[istation] = np.linalg.norm(spz)
else:
disp[istation,
0] = spz[0] * np.cos(dist) - spz[2] * np.sin(dist)
disp[istation, 1] = spz[1]
disp[istation,
2] = spz[0] * np.sin(dist) + spz[2] * np.cos(dist)
if args.norm:
vtk = pyvtk.VtkData(
vtk_points,
pyvtk.PointData(pyvtk.Scalars(disp_norm, name='disp_norm')),
'surface animation')
else:
vtk = pyvtk.VtkData(
vtk_points,
pyvtk.PointData(pyvtk.Vectors(disp, name='disp_RTZ')),
'surface animation')
vtk.tofile(args.out_vtk + '/surface_vtk.' + str(it) + '.vtk', 'binary')
if args.verbose:
print(' Done with snapshot t = %f s; tstep = %d / %d; iproc = %d' \
% (var_time[istep], it + 1, len(steps), iproc))
# close
nc_surf_local.close()
# remove temp nc
if args.nproc > 1:
os.remove(tempnc)
if args.verbose and iproc == 0:
elapsed = time.clock() - clock0
print('Generating snapshots done, ' + '%f sec elapsed.' % (elapsed))
#---------- </LOAD VARIABLES> ----------
#---------- <CREATE VTK FILE> ----------
wc = WavefieldComputer(wavefield, nu, s, z, sem_mesh)
for i_slice in range(SLICES):
x_slice, y_slice, z_slice, wvf_slice = wc.compute_slice(
RMIN[i_slice], RMAX[i_slice], PHIS_SLICES[i_slice])
points_slice = list(zip(x_slice, y_slice, z_slice))
range_slice = range(len(x_slice))
for it in range(num_steps):
vtk = pyvtk.VtkData(
pyvtk.UnstructuredGrid(points_slice, range_slice),
pyvtk.PointData(
pyvtk.Scalars(wvf_slice[it], name='wavefield_slice')),
'animation')
vtk.tofile(OUTPUT_DIR + 'slices/' + 'slice_' +
str(int(RMIN[i_slice] * 1.e-3)) + '_' +
str(int(RMAX[i_slice] * 1.e-3)) + '_' +
str(PHIS_SLICES[i_slice]) + '_' + str(it) + '.vtk')
### write info file for each slice
f = open(
OUTPUT_DIR + 'slices/'
'slice_' + str(int(RMIN[i_slice] * 1.e-3)) + '_' +
str(int(RMAX[i_slice] * 1.e-3)) + '_' + str(PHIS_SLICES[i_slice]) +
'_INFO.txt', 'w')
f.write('########## SLICE INFO ##########\n')
f.write('PHI (degrees) ' + str(PHIS_SLICES[i_slice]) + '\n')
f.write('RMIN (m) ' + str(RMIN[i_slice]) + '\n')
def _getStructure(self):
##maxX = self.distanceVar.mesh.faceCenters[0].max()
##minX = self.distanceVar.mesh.faceCenters[0].min()
IDs = numerix.nonzero(self.distanceVar._cellInterfaceFlag)[0]
coordinates = numerix.take(
numerix.array(self.distanceVar.mesh.cellCenters).swapaxes(0, 1),
IDs)
coordinates -= numerix.take(
numerix.array(self.distanceVar.grad * self.distanceVar).swapaxes(
0, 1), IDs)
coordinates *= self.zoomFactor
shiftedCoords = coordinates.copy()
shiftedCoords[:, 0] = -coordinates[:, 0] ##+ (maxX - minX)
coordinates = numerix.concatenate((coordinates, shiftedCoords))
from lines import _getOrderedLines
lines = _getOrderedLines(
range(2 * len(IDs)),
coordinates,
thresholdDistance=self.distanceVar.mesh._cellDistances.min() * 10)
data = numerix.take(self.surfactantVar, IDs)
data = numerix.concatenate((data, data))
tmpIDs = numerix.nonzero(data > 0.0001)[0]
if len(tmpIDs) > 0:
val = numerix.take(data, tmpIDs).min()
else:
val = 0.0001
data = numerix.where(data < 0.0001, val, data)
for line in lines:
if len(line) > 2:
for smooth in range(self.smooth):
for arr in (coordinates, data):
tmp = numerix.take(arr, line)
tmp[1:-1] = tmp[2:] * 0.25 + tmp[:-2] * 0.25 + tmp[
1:-1] * 0.5
if len(arr.shape) > 1:
for i in range(len(arr[0])):
arrI = arr[:, i].copy()
numerix.put(arrI, line, tmp[:, i])
arr[:, i] = arrI
else:
numerix.put(arrI, line, tmp)
name = self.title
name = name.strip()
if name == '':
name = None
coords = numerix.zeros((coordinates.shape[0], 3), 'd')
coords[:, :coordinates.shape[1]] = coordinates
import pyvtk
## making lists as pyvtk doesn't know what to do with numpy arrays
coords = list(coords)
coords = map(
lambda coord: [float(coord[0]),
float(coord[1]),
float(coord[2])], coords)
data = list(data)
data = map(lambda item: float(item), data)
return (pyvtk.UnstructuredGrid(points=coords, poly_line=lines),
pyvtk.PointData(pyvtk.Scalars(data, name=name)))
def save_scalar(self, s, name="my_field", step=0):
self.vtk_data.cell_data.append(pyvtk.Scalars(s, name))
# Compute the 2D Delaunay triangulation in the x-y plane
xTmp = list(zip(x, y))
tri = Delaunay(xTmp)
# Generate Cell Data
nCells = tri.nsimplex
cellTemp = np.random.rand(nCells)
# Zip the point co-ordinates for the VtkData input
points = list(zip(x, y, z))
vtk = pyvtk.VtkData(\
pyvtk.UnstructuredGrid(points,
triangle=tri.simplices
),
pyvtk.PointData(pyvtk.Scalars(pointPressure,name='Pressure')),
pyvtk.CellData(pyvtk.Scalars(cellTemp,name='Temperature')),
'2D Delaunay Example'
)
vtk.tofile('Delaunay2D')
vtk.tofile('Delaunay2Db', 'binary')
# Compute the 3D Delaunay triangulation in the x-y plane
xTmp = list(zip(x, y, z))
tri = Delaunay(xTmp)
# Generate Cell Data
nCells = tri.nsimplex
cellTemp = np.random.rand(nCells)
# Zip the point co-ordinates for the VtkData input
def write_vtk(iproc):
if args.nproc == 1:
nc_surf_local = Dataset(args.in_surface_nc, 'r', format='NETCDF4')
iproc = 0
else:
# copy netcdf file for parallel access
tempnc = args.out_vtk + '/surface_temp.nc' + str(iproc)
shutil.copy(args.in_surface_nc, tempnc)
nc_surf_local = Dataset(tempnc, 'r', format='NETCDF4')
# write vtk
if args.verbose and iproc == 0:
clock0 = time.clock()
print('Generating snapshot...')
for it, istep in enumerate(steps):
if it % args.nproc != iproc:
continue
if args.min_step is not None:
if it < args.min_step:
continue
if args.max_step is not None:
if it > args.max_step:
continue
disp_curl = np.zeros(nstation)
eleTag_last = -1
fourier_last = None
for istation, dist in enumerate(dists):
# poles cannot be computed correctly
if (dist < delta or dist > np.pi - delta):
disp_curl[istation] = 0.
continue
if eleTags[istation] == eleTag_last:
fourier = fourier_last
else:
fourier_r = nc_surf_local.variables['edge_' +
str(eleTags[istation]) +
'r'][istep, :]
fourier_i = nc_surf_local.variables['edge_' +
str(eleTags[istation]) +
'i'][istep, :]
fourier = fourier_r[:] + fourier_i[:] * 1j
fourier_last = fourier
eleTag_last = eleTags[istation]
nu_p_1 = int(len(fourier) / nPntEdge / 3)
wdotf = np.zeros((3, nu_p_1), dtype=fourier.dtype)
wdotf1 = np.zeros((3, nu_p_1), dtype=fourier.dtype)
for idim in np.arange(0, 3):
start = idim * nPntEdge * nu_p_1
end = idim * nPntEdge * nu_p_1 + nPntEdge * nu_p_1
fmat = fourier[start:end].reshape(nPntEdge, nu_p_1)
wdotf[idim] = weights[istation].dot(fmat)
wdotf1[idim] = weights1[istation].dot(fmat)
exparray = 2. * np.exp(np.arange(0, nu_p_1) * 1j * azims[istation])
exparray[0] = 1.
exparray1 = 2. * np.exp(
np.arange(0, nu_p_1) * 1j * (azims[istation] + delta))
exparray1[0] = 1.
spz = wdotf.dot(exparray).real
spz_dist1 = wdotf1.dot(exparray).real
spz_azim1 = wdotf.dot(exparray1).real
uR = spz[0] * np.cos(dist) - spz[2] * np.sin(dist)
uR_azim1 = spz_azim1[0] * np.cos(dist) - spz_azim1[2] * np.sin(
dist)
duR = (uR_azim1 - uR) / delta / np.sin(dist)
uT = spz[1]
uT_dist1 = spz_dist1[1]
duT = (uT_dist1 - uT) / (dists1[istation] - dist)
disp_curl[istation] = duR - duT
vtk = pyvtk.VtkData(
vtk_points,
pyvtk.PointData(pyvtk.Scalars(disp_curl, name='disp_curl')),
'surface animation')
vtk.tofile(args.out_vtk + '/surface_vtk_zcurl.' + str(it) + '.vtk',
'binary')
if args.verbose:
print(' Done with snapshot t = %f s; tstep = %d / %d; iproc = %d' \
% (var_time[istep], it + 1, len(steps), iproc))
# close
nc_surf_local.close()
# remove temp nc
if args.nproc > 1:
os.remove(tempnc)
if args.verbose and iproc == 0:
elapsed = time.clock() - clock0
print('Generating snapshots done, ' + '%f sec elapsed.' % (elapsed))
def ovf2vtk_main():
start_time = time.time()
banner_doc = 70 * "-" + \
"\novf2vtk --- converting ovf files to vtk files" + "\n" + \
"Hans Fangohr, Richard Boardman, University of Southampton\n"""\
+ 70 * "-"
# extracts command line arguments
# If any of the arguments given appear in the command line, a list of...
# ...these args and corresponding values (if any) is returned -> ('args').
# Any arguments that dont dont match the given ones are retuned in a...
# ...separate list -> ('params')
# Note (fangohr 30/12/2006 20:52): the use of getopt is historic,
args, params = getopt.getopt(sys.argv[1:], 'Vvhbta:', [
"verbose", "help", "add=", "binary", "text", "ascii",
"surface-effects", "version", "datascale=", "posscale="
])
# default value
surfaceEffects = False
datascale = 0.0 # 0.0 has special meaning -- see help text
posscale = 0.0 # 0.0 has special meaning -- see help text
# provide data from getopt.getopt (args) in form of dictionary
options = {}
for item in args:
if item[1] == '':
options[item[0]] = None
else:
options[item[0]] = item[1]
keys = options.keys()
# set system responses to arguments given
if "--surface-effects" in keys:
surfaceEffects = True
if "--posscale" in keys:
posscale = float(options["--posscale"])
if "--datascale" in keys:
datascale = float(options["--datascale"])
if "-v" in keys or "--verbose" in keys:
print("running in verbose mode")
debug = True
else:
debug = False
if "-h" in keys or "--help" in keys:
print(__doc__)
sys.exit(0)
if "-V" in keys or "--version" in keys:
print("This is version {:s}.".format(version))
sys.exit(0)
if len(params) == 0:
print(__doc__)
print("ERROR: An input file (and an output file need to be "
"specified).")
sys.exit(1)
else:
infile = params[0]
if len(params) == 1:
print(__doc__)
print("ERROR: An input file AND an output file need to be specified.")
print("specify output file")
sys.exit(1)
else:
outfile = params[1]
# okay: it seems the essential parameters are given.
# Let's check for others:
print(banner_doc)
if debug:
print("infile = {}".format(infile))
print("outfile = {}".format(outfile))
print("args = {}".format(args))
print("options = {}".format(options))
print("datascale = {}".format(datascale))
print("posscale = {}".format(posscale))
# read data from infile
vf = omf.read_structured_omf_file(infile, debug)
# compute magnitude for all cells
Ms = ana.magnitude(vf)
# Compute number of cells with non-zero Ms (rpb01r)
Ms_num_of_nonzeros = Numeric.sum(Numeric.not_equal(Ms, 0.0))
print("({:5.2f}% of {:d} cells filled)".format(
100.0 * Ms_num_of_nonzeros / len(Ms), len(Ms)))
# scale magnetisation data as required:
if datascale == 0.0:
scale = max(Ms)
print("Will scale data down by {:f}".format(scale))
else:
scale = datascale
# normalise vectorfield by scale
vf = Numeric.divide(vf, scale)
# read metadata in data file
ovf_run = omf.analyze(infile)
datatitle = ovf_run["Title:"] + "/{:g}".format(scale)
#
# need x, y and z vectors for vtk format
#
# taking actual spacings for dx, dy and dz results generally in
# poor visualisation results (in particular for thin films, one
# would like to have some magnification in z-direction). Also:vtk
# is not happy with positions on the 10e-9 scale, so one better
# scales this to something closer to unity.
# extract dimensions from file
dimensions = (int(ovf_run["xnodes:"]), int(ovf_run["ynodes:"]),
int(ovf_run["znodes:"]))
# scale data by given factor
if posscale != 0.0:
# find range between max and min values of components
xrange = abs(float(ovf_run["xmax:"]) - float(ovf_run["xmin:"]))
yrange = abs(float(ovf_run["ymax:"]) - float(ovf_run["ymin:"]))
zrange = abs(float(ovf_run["zmax:"]) - float(ovf_run["zmin:"]))
# define no. of x,y,z nodes
xnodes = float(ovf_run["xnodes:"])
ynodes = float(ovf_run["ynodes:"])
znodes = float(ovf_run["znodes:"])
# define stepsizes
xstepsize = float(ovf_run["xstepsize:"])
ystepsize = float(ovf_run["ystepsize:"])
zstepsize = float(ovf_run["zstepsize:"])
# define bases
xbase = float(ovf_run["xbase:"])
ybase = float(ovf_run["ybase:"])
zbase = float(ovf_run["zbase:"])
# find dx, dy, dz in SI units:
dx = xrange / xnodes
dy = yrange / ynodes
dz = zrange / znodes
# find scale factor that OOMMF uses for xstepsize and xnodes,
# etc. (Don't know how to get this directly.)
xscale = dx * xstepsize
yscale = dy * ystepsize
zscale = dz * zstepsize
# extract x, y and z positions from ovf file.
xbasevector = [None] * dimensions[0] # create empty vector
for i in range(dimensions[0]):
# data is stored for 'centre' of each cuboid, therefore (i+0.5)
xbasevector[i] = xbase + (i + 0.5) * xstepsize * xscale
ybasevector = [None] * dimensions[1]
for i in range(dimensions[1]):
ybasevector[i] = ybase + (i + 0.5) * ystepsize * yscale
zbasevector = [None] * dimensions[2]
for i in range(dimensions[2]):
zbasevector[i] = zbase + (i + 0.5) * zstepsize * zscale
# finally, convert list to numeric (need to have this consistent)
xbasevector = Numeric.array(xbasevector) / float(posscale)
ybasevector = Numeric.array(ybasevector) / float(posscale)
zbasevector = Numeric.array(zbasevector) / float(posscale)
else:
# posscale == 0.0
# this generally looks better:
xbasevector = Numeric.arange(dimensions[0])
ybasevector = Numeric.arange(dimensions[1])
zbasevector = Numeric.arange(dimensions[2])
#
# write ascii or binary vtk-file (default is binary)
#
vtk_data = 'binary'
if '--ascii' in keys or '-t' in keys or '--text' in keys:
vtk_data = 'ascii'
if debug:
print("switching to ascii vtk-data")
if '--binary' in keys or '-b' in keys:
vtk_data = 'binary'
if debug:
print("switching to binary vtk-data")
#
# and now open vtk-file
#
vtkfilecomment = "Output from ovf2vtk (version {:s}), {:s}, infile={:s}. "\
.format(version, time.asctime(), infile)
vtkfilecomment += "Calling command line was '{:s}' executed in '{:s}'"\
.format(" ".join(sys.argv), os.getcwd())
# define inputs
RecGrid = pyvtk.RectilinearGrid(xbasevector.tolist(), ybasevector.tolist(),
zbasevector.tolist())
PData = pyvtk.PointData(pyvtk.Vectors(vf.tolist(), datatitle))
# define vtk file.
vtk = pyvtk.VtkData(RecGrid, vtkfilecomment, PData, format=vtk_data)
# now compute all the additional data such as angles, etc
# check whether we should do all
keys = map(lambda x: x[1], args)
if "all" in keys:
args = []
for add_arg in add_features:
args.append(("--add", add_arg))
# when ovf2vtk was re-written using Numeric, I had to group
# certain operations to make them fast. Now some switches are
# unneccessary. (fangohr 25/08/2003 01:35)
# To avoid executing the
# same code again, we remember what we have computed already:
done_angles = 0
done_comp = 0
for arg in args:
if arg[0] == "-a" or arg[0] == "--add":
print("working on {}".format(arg))
data = []
lookup_table = 'default'
# compute observables that need more than one field value
# i.e. div, rot
if arg[1][0:6] == "divrot": # rotation = vorticity, curl
(div, rot, rotx, roty, rotz, rotmag) = \
ana.divergence_and_curl(vf, surfaceEffects, ovf_run)
# change order of observables for upcoming loop
observables = (rotx, roty, rotz, rotmag, rot, div)
comments = [
"curl, x-comp", "curl, y-comp", "curl, z-comp",
"curl, magnitude", "curl", "divergence"
]
# append data to vtk file
for obs, comment in zip(observables, comments):
# for rotx, roty, rotz, rotmag, div
if comment != "curl":
vtk.point_data.append(
pyvtk.Scalars(obs.tolist(), comment, lookup_table))
# for rot
else:
vtk.point_data.append(
pyvtk.Vectors(obs.tolist(), comment))
# components
elif arg[1] in ["Mx", "My", "Mz", "Ms"]:
if done_comp == 0:
done_comp = 1
comments = "x-component", "y-component", "z-component"
for data, comment in zip(ana.components(vf), comments):
vtk.point_data.append(
pyvtk.Scalars(data.tolist(), comment,
lookup_table))
# magnitude of magnitisation
Mmag = ana.magnitude(vf)
vtk.point_data.append(
pyvtk.Scalars(Mmag.tolist(), "Magnitude",
lookup_table))
elif arg[1] in ["xy", "xz", "yz"]:
if done_angles == 0:
done_angles = 1
# in-plane angles
comments = ("xy in-plane angle", "yz in-plane angle",
"xz in-plane angle")
for data, comment in zip(ana.plane_angles(vf), comments):
vtk.point_data.append(
pyvtk.Scalars(data.tolist(), comment,
lookup_table))
else:
print("only xy, xz, Mx, My, Mz, divergence, Ms, or 'all' \
allowed after -a or --add")
print("Current choice is {}".format(arg))
print(__doc__)
sys.exit(1)
#
# eventually, write the file
#
print("saving file ({:s})".format(outfile))
vtk.tofile(outfile, format=vtk_data)
print("finished conversion (execution time {:5.3s} seconds)".format(
str(time.time() - start_time)))
# generate the data.
from numpy import *
import scipy
x = (arange(50.0) - 25) / 2.0
y = (arange(50.0) - 25) / 2.0
r = sqrt(x**2 + y**2)
z = x * 5.0 * sin(x) # Bessel function of order 0
# now dump the data to a VTK file.
import pyvtk
# Flatten the 2D array data as per VTK's requirements.
z1 = reshape(transpose(z), (-1, ))
point_data = pyvtk.PointData(pyvtk.Scalars(z1))
grid = pyvtk.StructuredPoints((50, 50, 1), (-12.5, -12.5, 0), (0.5, 0.5, 1))
data = pyvtk.VtkData(grid, point_data)
data.tofile('/tmp/test.vtk')