# -*- python -*-
#
# Copyright INRIA - CIRAD - INRA
#
# Distributed under the Cecill-C License.
# See accompanying file LICENSE.txt or copy at
# http://www.cecill.info/licences/Licence_CeCILL-C_V1-en.html
#
# ==============================================================================
import operator
import vtk
import vtkmodules.util.numpy_support
# ==============================================================================
__all__ = [
"from_vertices_faces_to_vtk_poly_data",
"from_vtk_poly_data_to_vertices_faces",
"from_voxel_centers_to_vtk_image_data",
"from_numpy_matrix_to_vtk_image_data",
"from_vtk_image_data_to_voxels_center",
"voxel_grid_to_vtk_poly_data",
]
# ==============================================================================
[docs]
def voxel_grid_to_vtk_poly_data(voxel_grid):
"""
Get a vtkPolyData object from VoxelGrid object.
Parameters
-----------
voxel_grid: VoxelGrid
The voxel grid to transform.
Returns
-------
poly_data: vtk.vtkPolyData
A vtkPolyData object
"""
voxels_position = voxel_grid.voxels_position
voxels_size = voxel_grid.voxels_size
points = vtk.vtkPoints()
for v in voxels_position:
points.InsertNextPoint(v[0], v[1], v[2])
polydata = vtk.vtkPolyData()
polydata.SetPoints(points)
cube_source = vtk.vtkCubeSource()
cube_source.SetXLength(voxels_size)
cube_source.SetYLength(voxels_size)
cube_source.SetZLength(voxels_size)
glyph3_d = vtk.vtkGlyph3D()
if vtk.VTK_MAJOR_VERSION <= 5:
glyph3_d.SetSource(cube_source.GetOutput())
glyph3_d.SetInput(polydata)
else:
glyph3_d.SetSourceConnection(cube_source.GetOutputPort())
glyph3_d.SetInputData(polydata)
glyph3_d.Update()
return glyph3_d.GetOutput()
[docs]
def from_vertices_faces_to_vtk_poly_data(
vertices, faces, vertices_colors=None, faces_colors=None
):
"""
Get a vtkPolyData object from lists of vertices and faces.
Parameters
----------
vertices: list[tuple]
A list of tuple of vertex positions.
faces: list[tuple]
A list of tuple of faces id.
vertices_colors: list[tuple]
A list of RGB color tuple per vertices.
faces_colors: list[tuple]
A list of RGB color tuple per faces.
Returns
-------
poly_data: vtk.vtkPolyData
A vtkPolyData object.
"""
def make_vtk_id_list(it):
vil = vtk.vtkIdList()
for j in it:
vil.InsertNextId(int(j))
return vil
poly_data = vtk.vtkPolyData()
points = vtk.vtkPoints()
polys = vtk.vtkCellArray()
# Load the point, cell, and data attributes.
for i, vertex in enumerate(vertices):
points.InsertPoint(i, vertex)
for _, face in enumerate(faces):
polys.InsertNextCell(make_vtk_id_list(face))
# We now assign the pieces to the vtkPolyData.
poly_data.SetPoints(points)
del points
poly_data.SetPolys(polys)
del polys
if vertices_colors is not None:
vtk_colors = vtk.vtkUnsignedCharArray()
vtk_colors.SetNumberOfComponents(3)
vtk_colors.SetName("Colors")
for color in vertices_colors:
vtk_colors.InsertNextTuple3(color[0], color[1], color[2])
poly_data.GetPointData().SetScalars(vtk_colors)
if faces_colors is not None:
vtk_colors = vtk.vtkUnsignedCharArray()
vtk_colors.SetNumberOfComponents(3)
vtk_colors.SetName("Colors")
for color in faces_colors:
vtk_colors.InsertNextTuple3(color[0], color[1], color[2])
poly_data.GetCellData().SetScalars(vtk_colors)
return poly_data
[docs]
def from_vtk_poly_data_to_vertices_faces(vtk_poly_data):
"""
Get vertices and faces from a vtkPolyData object
Parameters
----------
vtk_poly_data: vtk.vtkPolyData
The vtkPolyData object to get info from
Returns
-------
mesh: tuple
A tuple containing vertices, faces and colors of the mesh
"""
vertices = vtkmodules.util.numpy_support.vtk_to_numpy(
vtk_poly_data.GetPoints().GetData()
)
faces = vtkmodules.util.numpy_support.vtk_to_numpy(
vtk_poly_data.GetPolys().GetData()
)
faces = faces.reshape((len(faces) // 4, 4))
colors = vtk_poly_data.GetPointData().GetScalars()
return vertices, faces[:, 1:], colors
[docs]
def from_numpy_matrix_to_vtk_image_data(data_matrix):
"""
Get a vtkImageData from a matrix.
Parameters
----------
data_matrix: numpy.matrix
The data matrix to get image info from.
Returns
-------
image_data: vtk.vtkImageData
A vtkImageData object with the matrix info.
"""
nx, ny, nz = data_matrix.shape
image_data = vtk.vtkImageData()
image_data.SetDimensions(nx, ny, nz)
image_data.SetSpacing(1.0, 1.0, 1.0)
if vtk.VTK_MAJOR_VERSION < 6:
image_data.SetScalarType(
vtkmodules.util.numpy_support.get_vtk_array_type(data_matrix.dtype)
)
image_data.SetNumberOfScalarComponents(1)
image_data.AllocateScalars()
else:
image_data.AllocateScalars(
vtkmodules.util.numpy_support.get_vtk_array_type(data_matrix.dtype), 1
)
lx, ly, lz = image_data.GetDimensions()
for i in range(lx):
for j in range(ly):
for k in range(lz):
image_data.SetScalarComponentFromDouble(
i, j, k, 0, data_matrix[i, j, k]
)
return image_data
[docs]
def from_vtk_image_data_to_voxels_center(image_data, true_value=255, component=0):
"""
Get voxels center from a vtkImageData object.
Parameters
----------
image_data: vtk.vtkImageData
The vtkImageData object.
true_value: int
component: int
Returns
-------
voxels_points: list
A list of voxel positions.
"""
dim_x, dim_y, dim_z = image_data.GetDimensions()
ori_x, ori_y, ori_z = image_data.GetOrigin()
spa_x, spa_y, spa_z = image_data.GetSpacing()
voxels_points = []
for x in range(dim_x):
for y in range(dim_y):
for z in range(dim_z):
r = image_data.GetScalarComponentAsDouble(x, y, z, component)
if r == true_value:
voxels_points.append(
(x * spa_x + ori_x, y * spa_y + ori_y, z * spa_z + ori_z)
)
return voxels_points
[docs]
def from_voxel_centers_to_vtk_image_data(voxel_centers, voxel_size):
"""
Get a vtkImageData object from a list of voxel centers.
Parameters
----------
voxel_centers: list[tuple]
A list of voxel centers.
voxel_size: int
The size each voxel.
Returns
-------
image_data: tuple
A tuple containing the vtkImageData object and the min voxel position
values.
"""
x_min = min(voxel_centers, key=operator.itemgetter(0))[0]
x_max = max(voxel_centers, key=operator.itemgetter(0))[0]
y_min = min(voxel_centers, key=operator.itemgetter(1))[1]
y_max = max(voxel_centers, key=operator.itemgetter(1))[1]
z_min = min(voxel_centers, key=operator.itemgetter(2))[2]
z_max = max(voxel_centers, key=operator.itemgetter(2))[2]
nx, ny, nz = (
int((x_max - x_min) / voxel_size + 1),
int((y_max - y_min) / voxel_size + 1),
int((z_max - z_min) / voxel_size + 1),
)
image_data = vtk.vtkImageData()
image_data.SetDimensions(nx, ny, nz)
image_data.SetSpacing(1.0, 1.0, 1.0)
if vtk.VTK_MAJOR_VERSION < 6:
image_data.SetScalarType(vtk.VTK_UNSIGNED_CHAR)
image_data.SetNumberOfScalarComponents(1)
image_data.AllocateScalars()
else:
image_data.AllocateScalars(vtk.VTK_DOUBLE, 0)
# Wrong initialization, image_data not initialize to 0 value
for x, y, z in voxel_centers:
nx = int((x - x_min) / voxel_size)
ny = int((y - y_min) / voxel_size)
nz = int((z - z_min) / voxel_size)
image_data.SetScalarComponentFromDouble(nx, ny, nz, 0, 1)
return image_data, (x_min, y_min, z_min)
