def _write_legacy_vtu(x, fname):
"""
Write a legacy VTK unstructured grid file.
"""
# Voxel local points relative to its centre of geometry:
voxel_local_points = asarray([[-1,-1,-1],[ 1,-1,-1],[-1, 1,-1],[ 1, 1,-1],
[-1,-1, 1],[ 1,-1, 1],[-1, 1, 1],[ 1, 1, 1]])\
* 0.5 # scaling
# Voxel world points:
points = []
# Culled input array -- as list:
xculled = []
try:
depth, rows, columns = x.shape
except ValueError:
sys.exit('Array dimensions not equal to 3, possibly 2-dimensional.\n')
for i in xrange(depth):
for j in xrange(rows):
for k in xrange(columns):
if x[i, j, k] > THRESHOLD:
xculled.append(x[i, j, k])
points += (voxel_local_points + [k, j, i]).tolist()
voxels = arange(len(points)).reshape(len(xculled), 8).tolist()
topology = UnstructuredGrid(points, voxel=voxels)
file_header = \
'ToPy data, created '\
+ str(datetime.now()).rsplit('.')[0]
scalars = CellData(Scalars(xculled, name='Densities', lookup_table =\
'default'))
vtk = VtkData(topology, file_header, scalars)
vtk.tofile(fname, 'binary')
def toVTK(self, fName, dx, dy, mask=False, clip=False, force=False, method='ct'):
""" Convert a 3D volume of interpolated values to vtk for visualization in Paraview """
print('toVTK')
self.getAttribute(xy=True, elevation=True, force=force)
self.getMean3D(dx=dx, dy=dy, mask=mask, clip=clip, force=force, method=method)
self.getZGrid()
self.points.getBounds()
x,y,intPoints = interpolation.getGridLocations2D(self.points.bounds, dx, dy)
z=self.zGrid
from pyvtk import VtkData, UnstructuredGrid, PointData, CellData, Scalars
# Get the 3D dimensions
mx = x.size
my = y.size
mz = z.size
nPoints = mx*my*mz
nCells = (mx-1)*(my-1)*(mz-1)
# Interpolate the elevation to the grid nodes
if (method == 'ct'):
tx,ty, vals = self.points.interpCloughTocher(self.elevation, dx = dx,dy=dy, mask = mask, clip = clip, extrapolate='nearest')
elif (method == 'mc'):
tx,ty, vals = self.points.interpMinimumCurvature(self.elevation, dx = dx, dy=dy, mask = mask, clip = clip)
vals = vals[:my,:mx]
vals = vals.reshape(mx*my)
# Set up the nodes and voxel indices
points = np.zeros([nPoints,3], order='F')
points[:,0] = np.tile(x,my*mz)
points[:,1] = np.tile(y.repeat(mx),mz)
points[:,2] = np.tile(vals,mz)-z.repeat(mx*my)
# Create the cell indices into the points
p = np.arange(nPoints).reshape((mz,my,mx))
voxels = np.zeros([nCells,8],dtype=np.int)
iCell = 0
for k in range(mz-1):
k1 = k + 1
for j in range(my-1):
j1 = j + 1
for i in range(mx-1):
i1 = i + 1
voxels[iCell,:] = [p[k1,j,i],p[k1,j,i1],p[k1,j1,i1],p[k1,j1,i], p[k,j,i],p[k,j,i1],p[k,j1,i1],p[k,j1,i]]
iCell += 1
# Create the various point data
pointID = Scalars(np.arange(nPoints),name='Point iD')
pointElev = Scalars(points[:,2],name='Point Elevation (m)')
tmp=self.mean3D.reshape(np.size(self.mean3D))
tmp1 = np.log10(1.0/tmp)
pointRes = Scalars(tmp1, name = 'log10(Resistivity) (Ohm m)')
tmp1 = np.log10(tmp)
pointCon = Scalars(tmp1, name = 'log10(Conductivity) (S/m)')
PData = PointData(pointID, pointElev, pointRes, pointCon)
CData = CellData(Scalars(np.arange(nCells),name='Cell iD'))
vtk = VtkData(
UnstructuredGrid(points,
hexahedron=voxels),
# ),
PData,
CData,
'Some Name'
)
vtk.tofile(fName, 'ascii')
def _data_item(is_cell_data, data, step):
sd = data[step, :]
if is_cell_data:
return CellData(Scalars(sd, 'cell_data', lookup_table='default'))
return PointData(Scalars(sd, 'vertex_data'))
def save_vtk(fname,
xyz,
triangles=None,
values=None,
vectors=None,
triangle_values=None):
"""Saves a point cloud or triangle mesh as a .vtk file.
Files can be opened with Paraview or displayed using the PyVista library.
Args:
fname (string): filename.
xyz (Tensor): (N,3) point cloud or vertices.
triangles (integer Tensor, optional): (T,3) mesh connectivity. Defaults to None.
values (Tensor, optional): (N,D) values, supported by the vertices. Defaults to None.
vectors (Tensor, optional): (N,3) vectors, supported by the vertices. Defaults to None.
triangle_values (Tensor, optional): (T,D) values, supported by the triangles. Defaults to None.
"""
# Encode the points/vertices as a VTK structure:
if triangles is None: # Point cloud
structure = PolyData(points=numpy(xyz), vertices=np.arange(len(xyz)))
else: # Surface mesh
structure = PolyData(points=numpy(xyz), polygons=numpy(triangles))
data = [structure]
pointdata, celldata = [], []
# Point values - one channel per column of the `values` array:
if values is not None:
values = numpy(values)
if len(values.shape) == 1:
values = values[:, None]
features = values.T
pointdata += [
Scalars(f, name=f"features_{i:02d}")
for i, f in enumerate(features)
]
# Point vectors - one vector per point:
if vectors is not None:
pointdata += [Vectors(numpy(vectors), name="vectors")]
# Store in the VTK object:
if pointdata != []:
pointdata = PointData(*pointdata)
data.append(pointdata)
# Triangle values - one channel per column of the `triangle_values` array:
if triangle_values is not None:
triangle_values = numpy(triangle_values)
if len(triangle_values.shape) == 1:
triangle_values = triangle_values[:, None]
features = triangle_values.T
celldata += [
Scalars(f, name=f"features_{i:02d}")
for i, f in enumerate(features)
]
celldata = CellData(*celldata)
data.append(celldata)
# Write to hard drive:
vtk = VtkData(*data)
os.makedirs(os.path.dirname(fname), exist_ok=True)
vtk.tofile(fname)