/usr/share/pyshared/viper/viper_dolfin.py is in python-viper 1.0.0-1.
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# Copyright (C) 2006-2011 Ola Skavhaug and Simula Research Laboratory
#
# This file is part of Viper.
#
# Viper is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# Viper is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public License
# along with Viper. If not, see <http://www.gnu.org/licenses/>.
__cite__ = """Ola Skavhaug, Viper Visualization Software,
http://www.fenicsproject.org"""
__version__ = "1.0.0"
__doc__ = """
Viper for DOLFIN
A simple mesh plotter and run--time visualization module for plotting and
saving simulation data. Adjusted Viper for plotting native DOLFIN data
structures like dolfin::Mesh, dolfin::MeshFunction, and dolfin::Function.
Citation: %s
""" % __cite__
from viper import Viper as ViperBase
import dolfin
from dolfin.cpp import Mesh, MeshFunctionInt, MeshFunctionUInt, MeshFunctionBool, MeshFunctionDouble, GenericFunction, Function, Expression, FunctionSpace, FunctionPlotData
import numpy
import vtk
import ffc
_plotter = None
plottable = [('mesh', (Mesh,)),
('genericfunction', (GenericFunction,)),
('functionplotdata', (FunctionPlotData,)),
('meshfunction', tuple(eval("MeshFunction%s" % t) for t in ["Int", "UInt", "Double", "Bool"]))]
class Viper(ViperBase):
"""A custom Viper sub-class for visualizing meshes and fields in Dolfin."""
def __init__(self, data, *args, **kwargs):
self._update = self.update
self.update = self.dolfin_update
kwargs["rescale"] = kwargs.get("rescale", True)
self.initcommon(kwargs)
self.warpscalar = True
self.lutfile = kwargs.get("lutfile", "gauss_120.lut")
self.plot(data, *args, **kwargs)
def parse_input(self, args, kwargs):
if len(args) == 1 and isinstance(args[0], str):
lst = [s.strip() for s in args[0].split(",")]
ar = []
kw = {}
for l in lst:
if "=" in l:
(k,v) = l.split("=")
kw[k] = eval(v)
else:
ar.append(eval(l))
return ar, kw
return args, kwargs
def plot(self, data, *args, **kwargs):
args, kwargs = self.parse_input(args, kwargs)
if "noninteractive" in args: kwargs["interactive"] = False
for plottype, classes in plottable:
if isinstance(data, classes):
self.plottype = plottype
plot_method = getattr(self, "plot_%s" % plottype)
plot_method(data, *args, **kwargs)
return
raise TypeError("Type not supported for plotting, %s" % str(type(data)))
def plot_mesh(self, data, *args, **kwargs):
self.rescale = False
self.mesh = data
self.vtkgrid = self.make_vtk_grid(self.mesh)
self.filter = self.vtkgrid
self.x = numpy.zeros(self.mesh.num_vertices())
(self.iren, self.renWin, self.ren) = self.simple_plotter(self.filter, self.x.min(), self.x.max(), wireframe=True)
self._update(self.x)
self.renWin.Render()
if kwargs.get("interactive", True):
self.interactive()
def plot_genericfunction(self, data, *args, **kwargs):
if isinstance(data, Expression):
self.mesh = kwargs.get("mesh")
if self.mesh is None or not isinstance(self.mesh, Mesh):
raise TypeError, "expected a mesh as kwargs when plotting Expression"
elif isinstance(data, Function):
self.mesh = data.function_space().mesh()
else:
raise TypeError, "Do not know how to plot the GenericFunction"
self.vtkgrid = self.make_vtk_grid(self.mesh)
self.filter = self.vtkgrid
self.warpscalar = kwargs.get("warpscalar", True)
self.rescale = kwargs.get("rescale", False)
self.mode = kwargs.get("mode", "auto")
wireframe=kwargs.get("wireframe", False)
self.pts = kwargs.get("eval_pts", None)
(dpn, rank) = self._dofs_pr_node(data)
if self.mode == "auto":
if dpn == 1:
if self.mesh.cells().shape[1] == 2:
self.mode = "scalar_xy"
else:
self.mode = "scalar"
elif dpn == self.mesh.geometry().dim():
self.mode = "vector"
else:
raise RuntimeError, "Can't plot function with %d dofs pr node" % dpn
if self.pts is None:
nno = self.mesh.num_vertices()
self.x = numpy.zeros(nno*dpn)
data.compute_vertex_values(self.x, self.mesh)
coords = self.mesh.coordinates()
else:
"""Only arbitrary point evaluation for vector valued functions."""
assert self.mode == "vector"
nno = len(self.pts)
self.x = numpy.zeros((nno,dpn))
v = numpy.zeros(dpn, dtype='d')
for (i, point) in enumerate(self.pts):
data.eval(v, point)
self.x[i,:] = v[:]
self.x = self.x.transpose().copy()
self.x.shape = nno*dpn,
coords = numpy.array(self.pts)
coords.shape = (len(self.pts), len(self.pts[0]))
vmin = kwargs.get("vmin", self.x.min())
vmax = kwargs.get("vmax", self.x.max())
assert vmax >= vmin, "Empty range, please specify vmin and/or vmax"
if self.mode == "scalar":
minmax = self.x.max() - self.x.min()
if self.warpscalar and minmax > 0 and self.mesh.geometry().dim() < 3:
self.filter = self.warp_scalar(self.x, minmax)
#self.__warping = True
(self.iren, self.renWin, self.ren) = self.simple_plotter(self.filter, vmin, vmax, wireframe=wireframe)
elif self.mode == "scalar_xy":
xx = self.mesh.coordinates()
(self.iren, self.renWin, self.ren) = self.plot_xy(xx, self.x, ".-",
vmin=kwargs.get("vmin", None),
vmax=kwargs.get("vmax", None))
elif self.mode in ("vector", "displacement"):
self.x.shape = (dpn, nno)
self.x = self.vec3d(self.x.transpose().copy())
if self.mode == "vector":
(self.iren, self.renWin, self.ren) = self.vector_plotter(coords, self.x, vmin, vmax, wireframe=False)
else:
self.displacement = self.x.copy()
# Use vector norms for scalar coloring
self.x = numpy.sqrt(self.x[:,0]**2 + self.x[:,1]**2 + self.x[:,2]**2)
self.filter = self.warp_vector(self.displacement)
(self.iren, self.renWin, self.ren) = self.simple_plotter(self.filter, vmin, vmax, wireframe=wireframe)
self.iren.Initialize()
self._update(self.x)
self.renWin.Render()
if kwargs.get("interactive", True):
self.interactive()
def plot_functionplotdata(self, data, *args, **kwargs):
self.mesh = data.mesh
self.vtkgrid = self.make_vtk_grid(self.mesh)
self.filter = self.vtkgrid
self.warpscalar = kwargs.get("warpscalar", True)
self.rescale = kwargs.get("rescale", False)
self.mode = kwargs.get("mode", "auto")
wireframe=kwargs.get("wireframe", False)
self.pts = kwargs.get("eval_pts", None)
rank = data.rank
dpn = 1
if rank > 0:
dpn = self.mesh.geometry().dim()
if self.mode == "auto":
if dpn == 1:
if self.mesh.cells().shape[1] == 2:
self.mode = "scalar_xy"
else:
self.mode = "scalar"
elif dpn == self.mesh.geometry().dim():
self.mode = "vector"
else:
raise RuntimeError, "Can't plot function with %d dofs pr node" % dpn
nno = self.mesh.num_vertices()
self.x = numpy.zeros(nno*dpn)
self.x = data.vertex_values().array().copy()
coords = self.mesh.coordinates()
vmin = kwargs.get("vmin", self.x.min())
vmax = kwargs.get("vmax", self.x.max())
assert vmax >= vmin, "Empty range, please specify vmin and/or vmax"
if self.mode == "scalar":
minmax = self.x.max() - self.x.min()
if self.warpscalar and minmax > 0 and self.mesh.geometry().dim() < 3:
self.filter = self.warp_scalar(self.x, minmax)
#self.__warping = True
(self.iren, self.renWin, self.ren) = self.simple_plotter(self.filter, vmin, vmax, wireframe=wireframe)
elif self.mode == "scalar_xy":
xx = self.mesh.coordinates()
(self.iren, self.renWin, self.ren) = self.plot_xy(xx, self.x, ".-",
vmin=kwargs.get("vmin", None),
vmax=kwargs.get("vmax", None))
elif self.mode in ("vector", "displacement"):
self.x.shape = (dpn, nno)
self.x = self.vec3d(self.x.transpose().copy())
if self.mode == "vector":
(self.iren, self.renWin, self.ren) = self.vector_plotter(coords, self.x, vmin, vmax, wireframe=False)
else:
self.displacement = self.x.copy()
# Use vector norms for scalar coloring
self.x = numpy.sqrt(self.x[:,0]**2 + self.x[:,1]**2 + self.x[:,2]**2)
self.filter = self.warp_vector(self.displacement)
(self.iren, self.renWin, self.ren) = self.simple_plotter(self.filter, vmin, vmax, wireframe=False)
self.iren.Initialize()
self._update(self.x)
self.renWin.Render()
if kwargs.get("interactive", True):
self.interactive()
def plot_meshfunction(self, data, *args, **kwargs):
self.mesh = data.mesh()
mesh_dim = self.mesh.topology().dim()
dim = data.dim()
size = data.size()
values = data.array()
self.vtkgrid = self.make_vtk_grid(self.mesh)
self.filter = self.vtkgrid
self.x = numpy.array(values, dtype='d')
if str(values.dtype).count("int"):
self.lutfile = ""
if dim in (0, mesh_dim-1, mesh_dim):
if dim==mesh_dim: # meshfunction over cells
self.vertex_plot = False
self.lutfile = ""
elif dim==mesh_dim-1: # meshfunction over faces
# Create a vertex valued meshfunction and plot that
self.mesh.init(dim)
vertices = type(data)(self.mesh, 0)
vertex_values = vertices.array()
vertex_values[:] = 0
con20 = self.mesh.topology()(dim,0)
for facet in xrange(self.mesh.num_faces()):
if values[facet]:
vertex_values[con20(facet)] = values[facet]
self.plot_meshfunction(vertices, *args, **kwargs)
return
(self.iren, self.renWin, self.ren) = self.simple_plotter(self.filter, self.x.min(), self.x.max(), wireframe=False)
else:
raise RuntimeError, "Only vertex, facets and cell valued meshfunctions can be plotted"
self.iren.Initialize()
self._update(self.x)
self.renWin.Render()
if kwargs.get("interactive", True):
self.interactive()
def _dofs_pr_node(self, f):
rank = f.value_rank()
dpn = 1
for i in xrange(rank):
dpn *= f.value_dimension(i)
return dpn, rank
def add_polygon(self, polygon, idx=0):
assert isinstance(polygon, (list, tuple))
numpoints = len(polygon)
assert isinstance(polygon[0], (list, tuple, numpy.ndarray))
points2d = False
if len(polygon[0]) == 2:
points2d = True
points = vtk.vtkPoints()
points.SetNumberOfPoints(numpoints)
for i in xrange(numpoints):
point = list(polygon[i])
if points2d:
point.append(0.0)
points.InsertPoint(i, *point)
line = vtk.vtkPolyLine()
line.GetPointIds().SetNumberOfIds(numpoints)
for i in xrange(numpoints):
line.GetPointIds().SetId(i, i)
grid = vtk.vtkUnstructuredGrid()
grid.Allocate(1, 1)
grid.InsertNextCell(line.GetCellType(),
line.GetPointIds())
grid.SetPoints(points)
extract = vtk.vtkGeometryFilter()
extract.SetInput(grid)
extract.GetOutput().ReleaseDataFlagOn()
self.polygon_data.AddInput(extract.GetOutput())
actor = self.polygon_actors[idx]
mapper = actor.GetMapper()
if mapper is None:
mapper = vtk.vtkPolyDataMapper()
actor.SetMapper(mapper)
mapper.SetInput(self.polygon_data.GetOutput())
actor.GetProperty().SetColor(0, 0, 1)
actor.GetProperty().SetLineWidth(1)
self.ren.AddActor(actor)
def dolfin_update(self, data, **kwargs):
# Prepare data to viper internal format
if self.plottype == "mesh":
self.mesh = data
self.vtkgrid = self.make_vtk_grid(self.mesh)
self.filter = self.vtkgrid
self.update_scalar_mapper(self.filter)
self.x = numpy.zeros(self.mesh.num_vertices())
elif self.plottype == "genericfunction":
(dpn, rank) = self._dofs_pr_node(data)
if self.pts is None:
nno = self.mesh.num_vertices()
self.x = numpy.zeros(nno*dpn)
data.compute_vertex_values(self.x, self.mesh)
else:
nno = len(self.pts)
self.x = numpy.zeros((nno,dpn))
v = numpy.zeros(dpn, dtype='d')
for (i, point) in enumerate(self.pts):
data.eval(v, point)
self.x[i,:] = v[:]
self.x = self.x.transpose().copy()
self.x.shape = nno*dpn,
if self.mode == "scalar":
minmax = self.x.max() - self.x.min()
if self.warpscalar and minmax > 0 and self.mesh.geometry().dim() < 3:
self.filter = self.warp_scalar(self.x, minmax)
if self.mode in ("vector", "displacement"):
self.x.shape = (dpn, nno)
self.x = self.vec3d(self.x.transpose().copy())
if self.mode == "displacement":
self.displacement[:] = self.x.copy()
self.x = numpy.sqrt(self.x[:,0]**2 + self.x[:,1]**2 + self.x[:,2]**2)
elif self.plottype == "meshfunction":
self.mesh = data.mesh()
self.vtkgrid = self.make_vtk_grid(self.mesh)
self.filter = self.vtkgrid
self.update_scalar_mapper(self.filter)
self.x = numpy.array(data.array(), dtype='d')
else:
print "Unknown plottype %s. Can't update" % (self.plottype,)
# Update title if given
if 'title' in kwargs:
self.title = str(kwargs['title'])
# Plot data
self._update(self.x)
class PlotManager(object):
def __init__(self):
import random
self.random = random
self.reset()
def figure(self, index):
self.index = index
def reset(self):
self.plots = {}
self.index = None # By default, use automatic plotting
def plot(self, plot_object, *args, **kwargs):
if self.index is None:
return self.autoplot(plot_object, *args, **kwargs)
return self.figureplot(plot_object, *args, **kwargs)
def autoplot(self, plot_object, *args, **kwargs):
for (idx, (plotter,obj)) in self.plots.items():
if obj is plot_object:
plotter.update(plot_object, **kwargs)
return plotter
idx = self.random.randint(0,10000)
keys = self.plots.keys()
while idx in keys:
idx = self.random.randint(0,10000)
kwargs["interactive"] = False
plotter = Viper(plot_object, *args, **kwargs)
self.plots[idx] = (plotter, plot_object)
return plotter
def figureplot(self, plot_object, *args, **kwargs):
if self.plots.has_key(self.index):
(plotter, obj) = self.plots[self.index]
plotter.update(plot_object, **kwargs)
self.plots[self.index] = (plotter, plot_object)
return plotter
kwargs["interactive"] = False
plotter = Viper(plot_object, *args, **kwargs)
self.plots[self.index] = (plotter, plot_object)
return plotter
def interactive(self):
if len(self.plots) > 0:
k = self.plots.keys()[0]
self.plots[k][0].interactive()
def figure(index):
global _plotter
if _plotter is None:
_plotter = PlotManager()
_plotter.figure(index)
def plot(data, *args, **kwargs):
global _plotter
if _plotter is None:
_plotter = PlotManager()
n_old_plots = len(_plotter.plots)
interactive = False
if kwargs.has_key("interactive"):
interactive = kwargs["interactive"]
kwargs["interactive"] = False
fig = _plotter.plot(data, **kwargs)
if n_old_plots > 0 and kwargs.get('autoposition', True):
x, y = fig.window_size
nx, ny = n_old_plots%3, n_old_plots//3
fig.renWin.SetPosition(nx*x, ny*y)
# The actual positioning seems to be indeterministic, but at least
# they don't overlap (completely).
#print (nx*x,ny*y), fig.renWin.GetPosition()
if interactive:
_plotter.interactive()
return fig
def update(data):
print "Not implemented"
return
global _viper
if _viper != None:
_viper.update(data)
return _viper
print "No plot object, cannot update"
def interactive():
global _plotter
if _plotter is None:
print "No plot object, interaction not possible"
return
_plotter.interactive()
def save_plot(u, filename="plot.png"):
v = Viper(u, interactive=False)
v.init_writer()
v.write_png(filename)
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