"""
Derived module from filehandler.py to handle vtk files.
.. warning::
This module will be deprecated in next releases. Follow updates on
https://github.com/mathLab for news about file handling.
"""
import numpy as np
import matplotlib.pyplot as plt
import mpl_toolkits.mplot3d as a3
import vtk
import pygem.filehandler as fh
import warnings
warnings.warn("This module will be deprecated in next releases", DeprecationWarning)
[docs]class VtkHandler(fh.FileHandler):
"""
Vtk file handler class
:cvar string infile: name of the input file to be processed.
:cvar string outfile: name of the output file where to write in.
:cvar list extensions: extensions of the input/output files. It
is equal to ['.vtk'].
"""
def __init__(self):
super(VtkHandler, self).__init__()
self.extensions = ['.vtk']
[docs] def parse(self, filename):
"""
Method to parse the file `filename`. It returns a matrix
with all the coordinates.
:param string filename: name of the input file.
:return: mesh_points: it is a `n_points`-by-3 matrix
containing the coordinates of the points of the mesh
:rtype: numpy.ndarray
.. todo::
- specify when it works
"""
self._check_filename_type(filename)
self._check_extension(filename)
self.infile = filename
reader = vtk.vtkDataSetReader()
reader.SetFileName(self.infile)
reader.ReadAllVectorsOn()
reader.ReadAllScalarsOn()
reader.Update()
data = reader.GetOutput()
n_points = data.GetNumberOfPoints()
mesh_points = np.zeros([n_points, 3])
for i in range(n_points):
mesh_points[i][0], mesh_points[i][1], mesh_points[i][
2] = data.GetPoint(i)
return mesh_points
[docs] def write(self, mesh_points, filename):
"""
Writes a vtk file, called filename, copying all the
structures from self.filename but the coordinates.
`mesh_points` is a matrix that contains the new coordinates
to write in the vtk file.
:param numpy.ndarray mesh_points: it is a `n_points`-by-3
matrix containing the coordinates of the points of the
mesh
:param string filename: name of the output file.
"""
self._check_filename_type(filename)
self._check_extension(filename)
self._check_infile_instantiation()
self.outfile = filename
reader = vtk.vtkDataSetReader()
reader.SetFileName(self.infile)
reader.ReadAllVectorsOn()
reader.ReadAllScalarsOn()
reader.Update()
data = reader.GetOutput()
points = vtk.vtkPoints()
for i in range(data.GetNumberOfPoints()):
points.InsertNextPoint(mesh_points[i, :])
data.SetPoints(points)
writer = vtk.vtkDataSetWriter()
writer.SetFileName(self.outfile)
writer.SetInputData(data)
writer.Write()
[docs] def plot(self, plot_file=None, save_fig=False):
"""
Method to plot a vtk file. If `plot_file` is not given it
plots `self.infile`.
:param string plot_file: the vtk filename you want to plot.
:param bool save_fig: a flag to save the figure in png or
not. If True the plot is not shown.
:return: figure: matlplotlib structure for the figure of
the chosen geometry
:rtype: matplotlib.pyplot.figure
"""
if plot_file is None:
plot_file = self.infile
else:
self._check_filename_type(plot_file)
# Read the source file.
reader = vtk.vtkDataSetReader()
reader.SetFileName(plot_file)
reader.Update()
data = reader.GetOutput()
points = data.GetPoints()
ncells = data.GetNumberOfCells()
# for each cell it contains the indeces of the points that define the cell
figure = plt.figure()
axes = a3.Axes3D(figure)
vtx = np.zeros((ncells, 3, 3))
for i in range(0, ncells):
for j in range(0, 3):
cell = data.GetCell(i).GetPointId(j)
vtx[i][j][0], vtx[i][j][1], vtx[i][j][2] = points.GetPoint(
int(cell))
tri = a3.art3d.Poly3DCollection([vtx[i]])
tri.set_color('b')
tri.set_edgecolor('k')
axes.add_collection3d(tri)
## Get the limits of the axis and center the geometry
max_dim = np.array(
[np.max(vtx[:, :, 0]),
np.max(vtx[:, :, 1]),
np.max(vtx[:, :, 2])])
min_dim = np.array(
[np.min(vtx[:, :, 0]),
np.min(vtx[:, :, 1]),
np.min(vtx[:, :, 2])])
max_lenght = np.max(max_dim - min_dim)
axes.set_xlim(-.6 * max_lenght + (max_dim[0] + min_dim[0]) / 2,
.6 * max_lenght + (max_dim[0] + min_dim[0]) / 2)
axes.set_ylim(-.6 * max_lenght + (max_dim[1] + min_dim[1]) / 2,
.6 * max_lenght + (max_dim[1] + min_dim[1]) / 2)
axes.set_zlim(-.6 * max_lenght + (max_dim[2] + min_dim[2]) / 2,
.6 * max_lenght + (max_dim[2] + min_dim[2]) / 2)
# Show the plot to the screen
if not save_fig:
plt.show()
else:
figure.savefig(plot_file.split('.')[0] + '.png')
return figure
[docs] def show(self, show_file=None):
"""
Method to show a vtk file. If `show_file` is not given
it shows `self.infile`.
:param string show_file: the vtk filename you want to show.
"""
if show_file is None:
show_file = self.infile
else:
self._check_filename_type(show_file)
# Read the source file.
reader = vtk.vtkUnstructuredGridReader()
reader.SetFileName(show_file)
reader.Update() # Needed because of GetScalarRange
output = reader.GetOutput()
scalar_range = output.GetScalarRange()
# Create the mapper that corresponds the objects of the vtk file
# into graphics elements
mapper = vtk.vtkDataSetMapper()
mapper.SetInputData(output)
mapper.SetScalarRange(scalar_range)
# Create the Actor
actor = vtk.vtkActor()
actor.SetMapper(mapper)
# Create the Renderer
renderer = vtk.vtkRenderer()
renderer.AddActor(actor)
# Set background color (white is 1, 1, 1)
renderer.SetBackground(20, 20, 20)
# Create the RendererWindow
renderer_window = vtk.vtkRenderWindow()
renderer_window.AddRenderer(renderer)
# Create the RendererWindowInteractor and display the vtk_file
interactor = vtk.vtkRenderWindowInteractor()
interactor.SetRenderWindow(renderer_window)
interactor.Initialize()
interactor.Start()