def to_vtk(self, prefix):
"""
export the result to vtk
the mesh and its triangle data go to prefix_name_mesh.vtk,
the potential/field/pseudopotential go to prefix_name.vtk
all arrays are named
"""
if self.configuration is not None:
self.configuration.to_vtk(prefix)
sp = tvtk.StructuredPoints(
origin=self.grid.get_origin(),
spacing=self.grid.step,
dimensions=self.grid.shape)
# spw = tvtk.StructuredPointsWriter(input=sp)
spw = tvtk.StructuredPointsWriter()
spw.set_input_data(sp)
spw.file_name = "%s_%s.vtk" % (prefix, self.configuration.name)
#xidr = tvtk.XMLImageDataWriter(input=sp)
for data_name in "potential field pseudo_potential".split():
data = getattr(self, data_name)
if data is None:
continue
if len(data.shape) > 3:
data = data.T.reshape(-1, data.shape[0])
else:
data = data.T.flatten()
d = tvtk.DoubleArray(name=data_name)
d.from_array(data)
sp.point_data.add_array(d)
spw.write()
logging.info("wrote %s", spw.file_name)
def transformNormals(t, pts):
"""Apply a vtkTransform to a numpy array of normals.
I.e. ignore the translation component and normalise
the resulting magnitudes"""
out = tvtk.DoubleArray(number_of_components=3)
t.transform_normals(pts, out)
return numpy.asarray(out)
def _get_vtk_data(self):
if self.position == 'nodes':
ug = self.vtk_node_structure
# vtk_r = self.vtk_node_points
# vtk_cell_data = self.vtk_node_cell_data
elif self.position == 'int_pnts':
ug = self.vtk_ip_structure
# vtk_r = self.custom_vtk_r
# vtk_cell_data = self.custom_vtk_cell_data
# ug = self.vtk_structure
field_arr = tvtk.DoubleArray(name=self.name)
field_arr.from_array(self._get_field_data()) # TODO:naming
ug.point_data.add_array(field_arr)
# add data for warping
if self.warp:
warp_arr = tvtk.DoubleArray(name=self.warp_var)
warp_arr.from_array(self._get_warp_data())
ug.point_data.add_array(warp_arr)
return ug
def get_rs_structured_grid(self, **args):
sg = tvtk.StructuredGrid()
arr0 = self.recip_arrs[list(self.recip_arrs.keys())[0]]
dims = list(arr0.shape)
sg.points = self.recip_coords
for a in self.recip_arrs.keys():
arr = tvtk.DoubleArray()
arr.from_array(self.recip_arrs[a].ravel())
arr.name = a
sg.point_data.add_array(arr)
sg.dimensions = (dims[2], dims[1], dims[0])
sg.extent = 0, dims[2] - 1, 0, dims[1] - 1, 0, dims[0] - 1
return sg
def to_polydata(self, **kwargs):
"""
return a vtk PolyData object for this mesh, add named cell_data arrays
from **kwargs (need to have same length as self.triangles)
"""
pd = tvtk.PolyData(points=self.points, polys=self.triangles)
e = tvtk.IntArray(name="electrode_index")
e.from_array(self.groups)
pd.cell_data.add_array(e)
for name, data in kwargs.items():
if data is None:
continue
c = tvtk.DoubleArray(name=name)
assert data.shape[0] == self.triangles.shape[0]
c.from_array(data)
pd.cell_data.add_array(c)
return pd
def get_structured_grid(self, **args):
self.update_coords()
dims = list(self.arr[self.cropobj].shape)
self.sg.points = self.coords
if args.has_key("mode"):
if args["mode"] == "Phase":
arr1 = self.arr[self.cropobj].ravel()
arr = (np.arctan2(arr1.imag, arr1.real))
else:
arr = np.abs(self.arr[self.cropobj].ravel())
else:
arr = self.arr[self.cropobj].ravel()
if (arr.dtype == np.complex128 or arr.dtype == np.complex64):
self.sg.point_data.scalars = np.abs(arr)
self.sg.point_data.scalars.name = "Amp"
ph = tvtk.DoubleArray()
ph.from_array(np.arctan2(arr.imag, arr.real))
ph.name = "Phase"
self.sg.point_data.add_array(ph)
else:
self.sg.point_data.scalars = arr
self.sg.dimensions = (dims[2], dims[1], dims[0])
self.sg.extent = 0, dims[2] - 1, 0, dims[1] - 1, 0, dims[0] - 1
return self.sg
# print 'sig_Emab', sig_Enab
delta23_ab = np.array([[1, 0, 0], [0, 1, 0]], dtype=np.float_)
cell_class = tvtk.Quad().cell_type
n_E, n_i, n_a = x_Eia.shape
n_Ei = n_E * n_i
points = np.einsum('Ia,ab->Ib', x_Eia.reshape(-1, n_c), delta23_ab)
ug = tvtk.UnstructuredGrid(points=points)
ug.set_cells(cell_class, np.arange(n_Ei).reshape(n_E, n_i))
vectors = np.einsum('Ia,ab->Ib', d_Eia.reshape(-1, n_c), delta23_ab)
ug.point_data.vectors = vectors
ug.point_data.vectors.name = 'displacement'
# Now view the data.
warp_arr = tvtk.DoubleArray(name='displacement')
warp_arr.from_array(vectors)
ug.point_data.add_array(warp_arr)
eps_Encd = tensors = np.einsum('...ab,ac,bd->...cd', eps_Enab, delta23_ab,
delta23_ab)
tensors = eps_Encd[:, :, [0, 1, 2, 0, 1, 2], [0, 1, 2, 1, 2, 0]].reshape(-1, 6)
tensors = eps_Encd.reshape(-1, 9)
ug.point_data.tensors = tensors
ug.point_data.tensors.name = 'strain'
@mayavi2.standalone
def view():
from mayavi.sources.vtk_data_source import VTKDataSource
from mayavi.modules.outline import Outline
def grapher(self):
g = nx.read_gpickle(self.subject_path)
g.remove_node(83)
position_key = "dn_position"
edge_key = "fa_mean"
node_label_key = "dn_fsname"
create_label = g.nodes()
#nodes of interest: 8, 18, 35, 37, 49, 59, 76, 78
nr_nodes = len(create_label)
position_array = np.zeros( (nr_nodes, 3) )
val_array = np.zeros((nr_nodes, 1))
for i,nodeid in enumerate(create_label):
#gives position of certain node
pos = g.node[nodeid][position_key]
pos = np.array(pos)
position_array[i,:] = pos
x, y, z = position_array[:,0], position_array[:,1], position_array[:,2]
edges = np.array(g.edges())
nr_edges = len(edges)
ev = np.zeros( (nr_edges, 1) )
for i,d in enumerate(g.edges_iter(data=True)):
ev[i] = d[2][edge_key]
assert d[0] == edges[i,0] and d[1] == edges[i,1]
edges=edges - 1
start_positions = position_array[edges[:, 0], :].T
end_positions = position_array[edges[:, 1], :].T
vectors = end_positions - start_positions
# Creates Edges
nodesource = mlab.pipeline.scalar_scatter(x, y, z, name = 'Node Source')
nodes = mlab.pipeline.glyph(nodesource, scale_factor=3.0, scale_mode='none', name = 'Nodes', mode='cube')
nodes.glyph.color_mode = 'color_by_scalar'
vectorsrc = mlab.pipeline.vector_scatter(start_positions[0],
start_positions[1],
start_positions[2],
vectors[0],
vectors[1],
vectors[2],
name = 'Connectivity Source')
da = tvtk.DoubleArray(name=edge_key)
da.from_array(ev)
vectorsrc.mlab_source.dataset.point_data.add_array(da)
vectorsrc.mlab_source.dataset.point_data.scalars = da.to_array()
vectorsrc.mlab_source.dataset.point_data.scalars.name = edge_key
vectorsrc.outputs[0].update()
thres = mlab.pipeline.threshold(vectorsrc, name="Thresholding")
#control appearance of edges and nodes (color vs size)
#how to mix and match color and size differences
myvectors = mlab.pipeline.vectors(thres,colormap='OrRd',
#mode='cylinder',
name='Connections',
scale_factor=1,
resolution=20,
# make the opacity of the actor depend on the scalar.
transparent=True,
scale_mode = 'vector')
myvectors.glyph.glyph_source.glyph_source.glyph_type = 'dash'
myvectors.glyph.color_mode = 'color_by_scalar'
myvectors.glyph.glyph.clamping = False
# create labels
for la in create_label:
row_index = la - 1
label = g.node[la][node_label_key]
mlab.text3d(position_array[row_index,0],
position_array[row_index,1],
position_array[row_index,2],
' ' + label,
name = 'Node ' + label,
color = (0,0,0),
scale = 3,
line_width = 3)
#Scales the nodes
for i,nodeid in enumerate(g.nodes()):
#nodes of interest: 8, 18, 35, 37, 49, 59, 76, 78
#if nodeid==8 or nodeid==18 or nodeid==35 or nodeid==37 or nodeid==49 or nodeid==59 or nodeid==76 or nodeid==78:
pos = g.node[nodeid][position_key]
val = g.degree(nodeid)
pos = np.array(pos)
val = np.array(val)
position_array[i,:] = pos
val_array[i] = val
x, y, z, value = position_array[:,0], position_array[:,1], position_array[:,2], val_array[:,0]
#mlab.figure()
mlab.points3d(x, y, z, value)
mlab.show()
def transformVectors(t, pts):
"""Apply a vtkTransform to a numpy array of vectors.
I.e. ignore the translation component"""
out = tvtk.DoubleArray(number_of_components=3)
t.transform_vectors(pts, out)
return numpy.asarray(out)