def add_polyhedron(self,
neighbors,
center,
color,
opacity=0.4,
draw_edges=False,
edges_color=[0.0, 0.0, 0.0],
edges_linewidth=2):
"""
Adds a polyhedron.
Args:
neighbors: Neighbors of the polyhedron (the vertices).
center: The atom in the center of the polyhedron.
color: Color for text as RGB.
opacity: Opacity of the polyhedron
draw_edges: If set to True, the a line will be drawn at each edge
edges_color: Color of the line for the edges
edges_linewidth: Width of the line drawn for the edges
"""
points = vtk.vtkPoints()
conv = vtk.vtkConvexPointSet()
for i in range(len(neighbors)):
x, y, z = neighbors[i].coords
points.InsertPoint(i, x, y, z)
conv.GetPointIds().InsertId(i, i)
grid = vtk.vtkUnstructuredGrid()
grid.Allocate(1, 1)
grid.InsertNextCell(conv.GetCellType(), conv.GetPointIds())
grid.SetPoints(points)
dsm = vtk.vtkDataSetMapper()
polysites = [center]
polysites.extend(neighbors)
self.mapper_map[dsm] = polysites
if vtk.VTK_MAJOR_VERSION <= 5:
dsm.SetInputConnection(grid.GetProducerPort())
else:
dsm.SetInputData(grid)
ac = vtk.vtkActor()
#ac.SetMapper(mapHull)
ac.SetMapper(dsm)
ac.GetProperty().SetOpacity(opacity)
if color == 'element':
# If partial occupations are involved, the color of the specie with
# the highest occupation is used
myoccu = 0.0
for specie, occu in center.species_and_occu.items():
if occu > myoccu:
myspecie = specie
myoccu = occu
color = [i / 255 for i in self.el_color_mapping[myspecie.symbol]]
ac.GetProperty().SetColor(color)
else:
ac.GetProperty().SetColor(color)
if draw_edges:
ac.GetProperty().SetEdgeColor(edges_color)
ac.GetProperty().SetLineWidth(edges_linewidth)
ac.GetProperty().EdgeVisibilityOn()
self.ren.AddActor(ac)
def add_polyhedron(self, neighbors, center, color):
"""
Adds a polyhedron.
Args:
neighbors:
Neighbors of the polyhedron (the vertices).
center:
The atom in the center of the polyhedron.
color:
Color for text as RGB.
"""
points = vtk.vtkPoints()
conv = vtk.vtkConvexPointSet()
for i in range(len(neighbors)):
x, y, z = neighbors[i].coords
points.InsertPoint(i, x, y, z)
conv.GetPointIds().InsertId(i, i)
grid = vtk.vtkUnstructuredGrid()
grid.Allocate(1, 1)
grid.InsertNextCell(conv.GetCellType(), conv.GetPointIds())
grid.SetPoints(points)
dsm = vtk.vtkDataSetMapper()
polysites = [center]
polysites.extend(neighbors)
self.mapper_map[dsm] = polysites
dsm.SetInput(grid)
ac = vtk.vtkActor()
#ac.SetMapper(mapHull)
ac.SetMapper(dsm)
ac.GetProperty().SetOpacity(0.4)
ac.GetProperty().SetColor(color)
self.ren.AddActor(ac)
def add_polyhedron(self, neighbors, center, color):
"""
Adds a polyhedron.
Args:
neighbors:
Neighbors of the polyhedron (the vertices).
center:
The atom in the center of the polyhedron.
color:
Color for text as RGB.
"""
points = vtk.vtkPoints()
conv = vtk.vtkConvexPointSet()
for i in range(len(neighbors)):
x, y, z = neighbors[i].coords
points.InsertPoint(i, x, y, z)
conv.GetPointIds().InsertId(i, i)
grid = vtk.vtkUnstructuredGrid()
grid.Allocate(1, 1)
grid.InsertNextCell(conv.GetCellType(), conv.GetPointIds())
grid.SetPoints(points)
dsm = vtk.vtkDataSetMapper()
polysites = [center]
polysites.extend(neighbors)
self.mapper_map[dsm] = polysites
dsm.SetInput(grid)
ac = vtk.vtkActor()
#ac.SetMapper(mapHull)
ac.SetMapper(dsm)
ac.GetProperty().SetOpacity(0.4)
ac.GetProperty().SetColor(color)
self.ren.AddActor(ac)
def add_polyhedron(self, neighbors, center, color, opacity=1.0,
draw_edges=False, edges_color=[0.0, 0.0, 0.0],
edges_linewidth=2):
"""
Adds a polyhedron.
Args:
neighbors: Neighbors of the polyhedron (the vertices).
center: The atom in the center of the polyhedron.
color: Color for text as RGB.
opacity: Opacity of the polyhedron
draw_edges: If set to True, the a line will be drawn at each edge
edges_color: Color of the line for the edges
edges_linewidth: Width of the line drawn for the edges
"""
points = vtk.vtkPoints()
conv = vtk.vtkConvexPointSet()
for i in range(len(neighbors)):
x, y, z = neighbors[i].coords
points.InsertPoint(i, x, y, z)
conv.GetPointIds().InsertId(i, i)
grid = vtk.vtkUnstructuredGrid()
grid.Allocate(1, 1)
grid.InsertNextCell(conv.GetCellType(), conv.GetPointIds())
grid.SetPoints(points)
dsm = vtk.vtkDataSetMapper()
polysites = [center]
polysites.extend(neighbors)
self.mapper_map[dsm] = polysites
if vtk.VTK_MAJOR_VERSION <= 5:
dsm.SetInputConnection(grid.GetProducerPort())
else:
dsm.SetInputData(grid)
ac = vtk.vtkActor()
#ac.SetMapper(mapHull)
ac.SetMapper(dsm)
ac.GetProperty().SetOpacity(opacity)
if color == 'element':
# If partial occupations are involved, the color of the specie with
# the highest occupation is used
myoccu = 0.0
for specie, occu in center.species_and_occu.items():
if occu > myoccu:
myspecie = specie
myoccu = occu
color = [i / 255 for i in self.el_color_mapping[myspecie.symbol]]
ac.GetProperty().SetColor(color)
else:
ac.GetProperty().SetColor(color)
if draw_edges:
ac.GetProperty().SetEdgeColor(edges_color)
ac.GetProperty().SetLineWidth(edges_linewidth)
ac.GetProperty().EdgeVisibilityOn()
self.ren.AddActor(ac)
def _2ugrid(e, ugrid=None):
"""
Convert element e to an unstructured grid
"""
# n, g, idx -- name, group and index in the group
# p -- array (Ns, Np, 3) of points
(n, g, idx), p = e
Ns, Np, _ = p.shape
if ugrid is None:
# Points
pl = vtk.vtkPoints()
# Grid
ug = vtk.vtkUnstructuredGrid()
# ug.Allocate(Ns - 1, 1)
ug.SetPoints(pl)
i0 = 0
else:
ug = ugrid
pl = ug.GetPoints()
i0 = pl.GetNumberOfPoints()
i = 0
for Is in range(Ns):
for Ip in range(Np):
pl.InsertPoint(i0 + i, p[Is, Ip, :])
i += 1
# Ns - 1 elements of the grid
for Is in range(Ns - 1):
ps = vtk.vtkConvexPointSet()
pids = ps.GetPointIds()
for i in range(2 * Np):
pids.InsertId(i, i0 + Is * Np + i)
ug.InsertNextCell(ps.GetCellType(), pids)
# Name and group to the Fields
if ugrid is None:
f = ug.GetFieldData()
f.AddArray(wrapStr(n, 'name'))
f.AddArray(wrapStr(g, 'group'))
return ug
attrs['associated_shape']
# delayed
mappers[shape_name] = (x for x in [mappers[associated_shape]()])
else:
reader = step_reader(str(io.shapes()[shape_name][:]))
readers[shape_name] = reader
mapper = vtk.vtkDataSetMapper()
add_compatiblity_methods(mapper)
mapper.SetInputConnection(reader.GetOutputPort())
mappers[shape_name] = (x for x in [mapper])
elif shape_type == 'convex':
# a convex shape
points = vtk.vtkPoints()
convex = vtk.vtkConvexPointSet()
data = io.shapes()[shape_name][:]
convex.GetPointIds().SetNumberOfIds(data.shape[0])
for id_, vertice in enumerate(io.shapes()[shape_name][:]):
points.InsertNextPoint(vertice[0], vertice[1], vertice[2])
convex.GetPointIds().SetId(id_, id_)
convex_grid = vtk.vtkUnstructuredGrid()
convex_grid.Allocate(1, 1)
convex_grid.InsertNextCell(convex.GetCellType(), convex.GetPointIds())
convex_grid.SetPoints(points)
source = vtk.vtkProgrammableSource()
def sourceExec():
output = source.GetUnstructuredGridOutput()
output.Allocate(1, 1)
# try to find an associated shape
if 'associated_shape' in io.shapes()[shape_name].attrs:
associated_shape = \
io.shapes()[shape_name].\
attrs['associated_shape']
# delayed
else:
reader = step_reader(str(io.shapes()[shape_name][:]))
readers[shape_name] = reader
elif shape_type == 'convex':
# a convex shape
points = vtk.vtkPoints()
convex = vtk.vtkConvexPointSet()
data = io.shapes()[shape_name][:]
convex.GetPointIds().SetNumberOfIds(data.shape[0])
for id_, vertice in enumerate(io.shapes()[shape_name][:]):
points.InsertNextPoint(vertice[0], vertice[1], vertice[2])
convex.GetPointIds().SetId(id_, id_)
readers[shape_name] = ConvexSource(convex, points)
else:
assert shape_type == 'primitive'
primitive = io.shapes()[shape_name].attrs['primitive']
attrs = io.shapes()[shape_name][:][0]
if primitive == 'Sphere':
source = vtk.vtkSphereSource()
def main():
cps = vtk.vtkConvexPointSet()
points = vtk.vtkPoints()
points.InsertNextPoint(0, 0, 0)
points.InsertNextPoint(1, 0, 0)
points.InsertNextPoint(1, 1, 0)
points.InsertNextPoint(0, 1, 0)
points.InsertNextPoint(0, 0, 1)
points.InsertNextPoint(1, 0, 1)
points.InsertNextPoint(1, 1, 1)
points.InsertNextPoint(0, 1, 1)
points.InsertNextPoint(0.5, 0, 0)
points.InsertNextPoint(1, 0.5, 0)
points.InsertNextPoint(0.5, 1, 0)
points.InsertNextPoint(0, 0.5, 0)
points.InsertNextPoint(0.5, 0.5, 0)
for i in range(0, 13):
cps.GetPointIds().InsertId(i, i)
ug = vtk.vtkUnstructuredGrid()
ug.Allocate(1, 1)
ug.InsertNextCell(cps.GetCellType(), cps.GetPointIds())
ug.SetPoints(points)
colors = vtk.vtkNamedColors()
mapper = vtk.vtkDataSetMapper()
mapper.SetInputData(ug)
actor = vtk.vtkActor()
actor.SetMapper(mapper)
actor.GetProperty().SetColor(colors.GetColor3d("Tomato"))
actor.GetProperty().SetLineWidth(3)
actor.GetProperty().EdgeVisibilityOn()
# Glyph the points
sphere = vtk.vtkSphereSource()
sphere.SetPhiResolution(21)
sphere.SetThetaResolution(21)
sphere.SetRadius(.03)
# Create a polydata to store everything in
polyData = vtk.vtkPolyData()
polyData.SetPoints(points)
pointMapper = vtk.vtkGlyph3DMapper()
pointMapper.SetInputData(polyData)
pointMapper.SetSourceConnection(sphere.GetOutputPort())
pointActor = vtk.vtkActor()
pointActor.SetMapper(pointMapper)
pointActor.GetProperty().SetColor(colors.GetColor3d("Peacock"))
# Create a renderer, render window, and interactor
renderer = vtk.vtkRenderer()
renderWindow = vtk.vtkRenderWindow()
renderWindow.SetWindowName("ConvexPointSet")
renderWindow.AddRenderer(renderer)
renderWindowInteractor = vtk.vtkRenderWindowInteractor()
renderWindowInteractor.SetRenderWindow(renderWindow)
# Add the actors to the scene
renderer.AddActor(actor)
renderer.AddActor(pointActor)
renderer.SetBackground(colors.GetColor3d("Silver"))
renderer.ResetCamera()
renderer.GetActiveCamera().Azimuth(210)
renderer.GetActiveCamera().Elevation(30)
renderer.ResetCameraClippingRange()
# Render and interact
renderWindow.SetSize(640, 480)
renderWindow.Render()
renderWindowInteractor.Start()