def toVTK(self, fileName, pointData=None, cellData=None, format='binary'):
"""Save to a VTK file.
Parameters
----------
fileName : str
Filename to save to.
pointData : geobipy.StatArray or list of geobipy.StatArray, optional
Data at each node in the mesh. Each entry is saved as a separate
vtk attribute.
cellData : geobipy.StatArray or list of geobipy.StatArray, optional
Data at each cell in the mesh. Each entry is saved as a separate
vtk attribute.
format : str, optional
"ascii" or "binary" format. Ascii is readable, binary is not but results in smaller files.
Raises
------
TypeError
If pointData or cellData is not a geobipy.StatArray or list of them.
ValueError
If any pointData (cellData) entry does not have size equal to the number of points (cells).
ValueError
If any StatArray does not have a name or units. This is needed for the vtk attribute.
"""
vtk = self.vtkStructure()
if not pointData is None:
assert isinstance(pointData, (StatArray, list)), TypeError("pointData must a geobipy.StatArray or a list of them.")
if isinstance(pointData, list):
for p in pointData:
assert isinstance(p, StatArray), TypeError("pointData entries must be a geobipy.StatArray")
assert all(p.shape == [self.z.nEdges, self.x.nEdges]), ValueError("pointData entries must have shape {}".format([self.z.nEdges, self.x.nEdges]))
assert p.hasLabels(), ValueError("StatArray needs a name")
vtk.point_data.append(Scalars(p.reshape(self.nNodes), p.getNameUnits()))
else:
assert all(pointData.shape == [self.z.nEdges, self.x.nEdges]), ValueError("pointData entries must have shape {}".format([self.z.nEdges, self.x.nEdges]))
assert pointData.hasLabels(), ValueError("StatArray needs a name")
vtk.point_data.append(Scalars(pointData.reshape(self.nNodes), pointData.getNameUnits()))
if not cellData is None:
assert isinstance(cellData, (StatArray, list)), TypeError("cellData must a geobipy.StatArray or a list of them.")
if isinstance(cellData, list):
for p in cellData:
assert isinstance(p, StatArray), TypeError("cellData entries must be a geobipy.StatArray")
assert all(p.shape == self.dims), ValueError("cellData entries must have shape {}".format(self.dims))
assert p.hasLabels(), ValueError("StatArray needs a name")
vtk.cell_data.append(Scalars(p.reshape(self.nCells), p.getNameUnits()))
else:
assert all(cellData.shape == self.dims), ValueError("cellData entries must have shape {}".format(self.dims))
assert cellData.hasLabels(), ValueError("StatArray needs a name")
vtk.cell_data.append(Scalars(cellData.reshape(self.nCells), cellData.getNameUnits()))
vtk.tofile(fileName, format)
def toVTK(self, fileName, pointData=None, format='binary'):
"""Save the PointCloud3D to a VTK file.
Parameters
----------
fileName : str
Filename to save to.
pointData : geobipy.StatArray or list of geobipy.StatArray, optional
Data at each point in the point cloud. Each entry is saved as a separate
vtk attribute.
format : str, optional
"ascii" or "binary" format. Ascii is readable, binary is not but results in smaller files.
Raises
------
TypeError
If pointData is not a geobipy.StatArray or list of them.
ValueError
If any pointData entry does not have size equal to the number of points.
ValueError
If any StatArray does not have a name or units. This is needed for the vtk attribute.
"""
vtk = self.vtkStructure()
if not pointData is None:
assert isinstance(
pointData, (StatArray.StatArray, list)), TypeError(
"pointData must a geobipy.StatArray or a list of them.")
if isinstance(pointData, list):
for p in pointData:
assert isinstance(p, StatArray.StatArray), TypeError(
"pointData entries must be a geobipy.StatArray")
assert p.size == self.nPoints, ValueError(
"pointData entries must have size {}".format(
self.nPoints))
assert p.hasLabels(), ValueError("StatArray needs a name")
vtk.point_data.append(Scalars(p, p.getNameUnits()))
else:
assert pointData.size == self.nPoints, ValueError(
"pointData entries must have sizd {}".format(self.nPoints))
assert pointData.hasLabels(), ValueError(
"StatArray needs a name")
vtk.point_data.append(
Scalars(pointData, pointData.getNameUnits()))
vtk.tofile(fileName, format=format)
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 save_vtk(fname, points, colors):
"""N.B.: Paraview is a good VTK viewer, which supports ray-tracing."""
structure = PolyData(points=points, vertices=np.arange(len(points)))
values = PointData(Scalars(colors, name="colors"))
vtk = VtkData(structure, values)
vtk.tofile(folder + fname, "binary")
def add_data(self, vtkfile, scalars=[], vectors=[], scale_factor=1):
from pyvtk import Scalars, Vectors
vtkfile.pointdata.extend(
Scalars(np.array(scale_factor * field),
name=name,
lookup_table="default") for name, field in scalars)
vtkfile.pointdata.extend(
Vectors([_three_vector(scale_factor * v) for v in zip(field)],
name=name) for name, field in vectors)
def vtkStructure(self):
"""Generates a vtk mesh structure that can be used in a vtk file.
Returns
-------
out : pyvtk.VtkData
Vtk data structure
"""
nodes = np.vstack([self.x, self.y, self.z]).T
vtk = VtkData(UnstructuredGrid(nodes, vertex=np.arange(self._nPoints)))
vtk.point_data.append(Scalars(self.z, self.z.getNameUnits()))
return vtk
def patched_scalars_fromfile(f, n, sl):
dataname = sl[0]
datatype = sl[1].lower()
assert datatype in [
'bit', 'unsigned_char', 'char', 'unsigned_short', 'short',
'unsigned_int', 'int', 'unsigned_long', 'long', 'float', 'double'
], repr(datatype)
if len(sl) > 2:
numcomp = eval(sl[2])
else:
numcomp = 1
l = common._getline(f)
l = l.split()
assert len(l) == 2 and l[0].lower().decode('UTF-8') == 'lookup_table'
tablename = l[1].decode('UTF-8')
scalars = []
while len(scalars) < n:
scalars += list(map(eval, common._getline(f).split()))
assert len(scalars) == n
return Scalars(scalars, dataname, tablename)
def addToVTK(self, vtk, prop=['data', 'predicted', 'std'], system=None):
"""Adds a member to a VTK handle.
Parameters
----------
vtk : pyvtk.VtkData
vtk handle returned from self.vtkStructure()
prop : str or list of str, optional
List of the member to add to a VTK handle, either "data", "predicted", or "std".
system : int, optional
The system for which to add the data
"""
if isinstance(prop, str):
prop = [prop]
for p in prop:
assert p in [
'data', 'predicted', 'std'
], ValueError("prop must be either 'data', 'predicted' or 'std'.")
if p == "data":
tmp = self.data
elif p == "predicted":
tmp = self.predictedData
elif p == "std":
tmp = self.std
if system is None:
r = range(self.nChannels)
else:
assert system < self.nSystems, ValueError(
"system must be < nSystems {}".format(self.nSystems))
r = range(self._systemOffset[system],
self._systemOffset[system + 1])
for i in r:
vtk.point_data.append(
Scalars(
tmp[:, i], "{} {}".format(self.channelNames[i],
tmp.getNameUnits())))
def write_vtk(filename, points, tetra, vals, name=None):
"""Writes a vtk from the given set of grid locations, values and connectivity
:param points: An ndarray containing all the grid locations in cartesion coordinates
in the form of: | x0 y0 z0 |
| : : : |
| xn yn zn |
:param vals: an array containing the values to be specified on the mesh
:param tetra: connectivity of the mesh
"""
import pyvtk
from pyvtk import PointData, Scalars
vtkElements = pyvtk.VtkData(
pyvtk.UnstructuredGrid(
points,
tetra=tetra),
PointData(Scalars(vals, name)),
"Mesh")
vtkElements.tofile(filename)
def runner(parser, options, args):
if not hasattr(parser, 'runner'):
options.output_path = None
if args:
if len(args) == 1:
if options.input_path:
print >> sys.stderr, "WARNING: overwriting input path %r with %r" % (
options.input_path, args[0])
options.input_path = args[0]
elif len(args) == 2:
if options.input_path:
print >> sys.stderr, "WARNING: overwriting input path %r with %r" % (
options.input_path, args[0])
options.input_path = args[0]
if options.output_path:
print >> sys.stderr, "WARNING: overwriting output path %r with %r" % (
options.output_path, args[1])
options.output_path = args[1]
else:
parser.error(
"Incorrect number of arguments (expected upto 2 but got %s)" %
(len(args)))
if options.input_path is None:
parser.error('Expected --input-path but got nothing')
options.input_path = fix_path(options.input_path)
stack = ImageStack.load(options.input_path, options=options)
numpy_types = numpy.typeDict.values()
if options.output_type in ['<detect>', None]:
if str(stack.images.dtype).startswith('float'):
output_type_name = 'float32'
elif str(stack.images.dtype).startswith('int'):
output_type_name = 'int32'
elif str(stack.images.dtype).startswith('uint'):
output_type_name = 'uint32'
else:
output_type_name = 'int32'
else:
output_type_name = options.output_type.lower()
output_type = getattr(numpy, output_type_name, None)
mn, mx = stack.images.min(), stack.images.max()
print 'Input minimum and maximum: %s, %s' % (mn, mx)
if options.scale and 'int' in output_type_name:
tmn, tmx = get_dtype_min_max(output_type)
new_images = (tmn + float(tmx - tmn) * (stack.images - float(mn)) /
(mx - mn)).astype(output_type)
else:
new_images = stack.images.astype(output_type)
print 'Output minimum and maximum: %s, %s' % (new_images.min(),
new_images.max())
output_path = options.output_path
output_ext = options.output_ext
if output_path is None:
dn = os.path.dirname(options.input_path)
bn = os.path.basename(options.input_path)
if os.path.isfile(options.input_path):
fn, ext = os.path.splitext(bn)
type_part = None
for t in numpy_types:
if fn.endswith('_' + t.__name__):
type_part = t.__name__
break
if type_part is None:
output_path = os.path.join(
dn, fn + '_' + output_type_name + '.' + output_ext)
else:
output_path = os.path.join(
dn,
fn[:-len(type_part)] + output_type_name + '.' + output_ext)
elif os.path.isdir(options.input_path):
output_path = os.path.join(
dn, bn + '_' + output_type_name + '.' + output_ext)
else:
raise NotImplementedError('%s is not file nor directory' %
(options.input_path))
output_path = fix_path(output_path)
print 'Saving new stack to', output_path
if output_ext == 'tif':
ImageStack(new_images, stack.pathinfo,
options=options).save(output_path)
elif output_ext == 'data':
from iocbio.microscope.psf import normalize_unit_volume, discretize
value_resolution = stack.pathinfo.get_value_resolution()
normal_images = normalize_unit_volume(new_images,
stack.get_voxel_sizes())
discrete = discretize(new_images / value_resolution)
signal_indices = numpy.where(discrete > 0)
new_value_resolution = value_resolution * normal_images.max(
) / new_images.max()
ImageStack(normal_images,
stack.pathinfo,
value_resolution=new_value_resolution).save(
output_path, zip(*signal_indices))
elif output_ext == 'vtk':
from pyvtk import VtkData, StructuredPoints, PointData, Scalars
vtk = VtkData(StructuredPoints(new_images.shape),
PointData(Scalars(new_images.T.ravel())))
vtk.tofile(output_path, 'binary')
else:
raise NotImplementedError( ` output_ext `)
get_size()
to_string(format = 'ascii')
append(<DataSetAttr instance>)
"""
data_type = 'POINT_DATA'
class CellData(Data):
"""
Usage:
CellData(<DataSetAttr instances>)
Attributes:
data - list of DataSetAttr instances
Public methods:
get_size()
to_string(format = 'ascii')
append(<DataSetAttr instance>)
"""
data_type = 'CELL_DATA'
def is_pointdata(obj):
return isinstance(obj,PointData)
def is_celldata(obj):
return isinstance(obj,CellData)
if __name__ == "__main__":
print(PointData(Scalars.Scalars([2,3])))
def Scalars(self,func,name = None,lookup_table = None):
return Scalars.Scalars([func(*p) for p in self.get_points()],name,lookup_table)
#============================================================
#- Triangulation.
#============================================================
for i in range(0, m.shape[0]):
S = m[i, :]
outfile = outfilename + '.' + str(i) + '.vtk'
print('Compute Delauney triangulation ...')
x = 6371.0 * np.cos(lat * np.pi / 180.0) * np.cos(lon * np.pi / 180.0)
y = 6371.0 * np.cos(lat * np.pi / 180.0) * np.sin(lon * np.pi / 180.0)
z = 6371.0 * np.sin(lat * np.pi / 180.0)
pts = np.array((x, y, z)).T
mesh_info = MeshInfo()
mesh_info.set_points(pts)
opts = Options("Q")
mesh = build(mesh_info, options=opts)
elements = mesh.elements
#============================================================
#- Write vtk file.
#============================================================
print('Write vtk file ...')
vtkElements = pyvtk.VtkData(pyvtk.UnstructuredGrid(pts, tetra=elements),
PointData(Scalars(S, 'grad_PSD_ZZ')), "Mesh")
vtkElements.tofile(outfile)
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 runner (parser, options, args):
if not hasattr(parser, 'runner'):
options.output_path = None
if args:
if len (args)==1:
if options.input_path:
print >> sys.stderr, "WARNING: overwriting input path %r with %r" % (options.input_path, args[0])
options.input_path = args[0]
elif len(args)==2:
if options.input_path:
print >> sys.stderr, "WARNING: overwriting input path %r with %r" % (options.input_path, args[0])
options.input_path = args[0]
if options.output_path:
print >> sys.stderr, "WARNING: overwriting output path %r with %r" % (options.output_path, args[1])
options.output_path = args[1]
else:
parser.error("Incorrect number of arguments (expected upto 2 but got %s)" % (len(args)))
if options.input_path is None:
parser.error('Expected --input-path but got nothing')
options.input_path = fix_path (options.input_path)
stack = ImageStack.load(options.input_path, options=options)
numpy_types = numpy.typeDict.values()
if options.output_type in ['<detect>', None]:
output_type_name = stack.images.dtype.name
else:
output_type_name = options.output_type.lower()
output_type = getattr (numpy, output_type_name, None)
nof_stacks = stack.get_nof_stacks()
old_shape = stack.images.shape
new_shape = (nof_stacks, old_shape[0]//nof_stacks) + old_shape[1:]
new_images = numpy.zeros (new_shape[1:], dtype=output_type_name)
first_stack = None
last_stack = None
for i, stacki in enumerate(stack.images.reshape(new_shape)):
if i==0:
first_stack = stacki.astype (float)
new_images[:] = stacki
else:
err_first = abs(stacki - first_stack).mean()
err_last = abs(stacki - last_stack).mean()
print ('Stack %i: mean abs difference from first and last stack: %.3f, %.3f' % (i+1, err_first, err_last))
new_images += stacki
last_stack = stacki.astype(float)
output_path = options.output_path
output_ext = options.output_ext
if output_path is None:
dn = os.path.dirname(options.input_path)
bn = os.path.basename(options.input_path)
if os.path.isfile(options.input_path):
fn, ext = os.path.splitext (bn)
fn += '_sumstacks%s' % (nof_stacks)
type_part = None
for t in numpy_types:
if fn.endswith('_' + t.__name__):
type_part = t.__name__
break
if type_part is None:
output_path = os.path.join(dn, fn + '_' + output_type_name + '.' + output_ext)
else:
output_path = os.path.join(dn, fn[:-len(type_part)] + output_type_name + '.' + output_ext)
elif os.path.isdir (options.input_path):
bn += '_sumstacks%s' % (nof_stacks)
output_path = os.path.join (dn, bn+'_'+output_type_name + '.' + output_ext)
else:
raise NotImplementedError ('%s is not file nor directory' % (options.input_path))
output_path = fix_path(output_path)
print 'Saving new stack to',output_path
if output_ext=='tif':
ImageStack(new_images, stack.pathinfo, options=options).save(output_path)
elif output_ext=='data':
from iocbio.microscope.psf import normalize_unit_volume, discretize
value_resolution = stack.pathinfo.get_value_resolution()
normal_images = normalize_unit_volume(new_images, stack.get_voxel_sizes())
discrete = discretize(new_images / value_resolution)
signal_indices = numpy.where(discrete>0)
new_value_resolution = value_resolution * normal_images.max() / new_images.max()
ImageStack(normal_images, stack.pathinfo,
value_resolution = new_value_resolution).save(output_path, zip(*signal_indices))
elif output_ext=='vtk':
from pyvtk import VtkData, StructuredPoints, PointData, Scalars
vtk = VtkData (StructuredPoints (new_images.shape), PointData(Scalars(new_images.T.ravel())))
vtk.tofile(output_path, 'binary')
else:
raise NotImplementedError (`output_ext`)
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')
# -2, -2, -2, -2, +2, -2, +2, +2, -2, +2, -2, -2, -2, -2, +2, +2, -2,
# +2, +2, +2, +2, -2, +2, +2;
#
# specfem = Specfem(interp_method='trilinear_interpolation')
# first_element = specfem.connectivity[0,:]
# element_vtcs = specfem.nodes[first_element]
#
# permutation = [0,3,2,1,4,5,6,7] # looks like this is the correct one
# i = np.argsort(permutation)
# element_perturbed = first_element[i]
# element_vtcs = specfem.nodes[element_perturbed]
#
# #pnt = np.mean(element_vtcs, axis=0)
# pnt = (element_vtcs[4,:] + element_vtcs[6,:]) / 2
# solution = tlp.check_hull(pnt, element_vtcs)
# print(solution)
# print(tlp.interpolate_at_point(solution[1]))
#
import pyvtk
from pyvtk import PointData, Scalars
vtkElements = pyvtk.VtkData(pyvtk.UnstructuredGrid(
specfem.nodes, hexahedron=specfem.connectivity),
PointData(Scalars(grid_data.get_component('vsv'), 'node_number')),
"Mesh")
vtkElements.tofile('specfem_mesh.vtk')
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)