def test_interpolation(self):
from sfepy import data_dir
from sfepy.discrete.fem import Mesh
from sfepy.linalg import make_axis_rotation_matrix
fname = in_dir(self.options.out_dir)
meshes = {
'tp' : Mesh.from_file(data_dir + '/meshes/3d/block.mesh'),
'si' : Mesh.from_file(data_dir + '/meshes/3d/cylinder.mesh'),
}
datas = gen_datas(meshes)
for field_name in ['scalar_si', 'vector_si', 'scalar_tp', 'vector_tp']:
m1 = meshes[field_name[-2:]]
for ia, angle in enumerate(nm.linspace(0.0, nm.pi, 11)):
self.report('%s: %d. angle: %f' % (field_name, ia, angle))
shift = [0.0, 0.0, 0.0]
mtx = make_axis_rotation_matrix([0, 1, 0], angle)
m2 = m1.copy('rotated mesh')
m2.transform_coors(mtx)
data = datas[field_name]
u1, u2 = do_interpolation(m2, m1, data, field_name)
if ia == 0:
u1.save_as_mesh(fname('test_mesh_interp_%s_u1.vtk'
% field_name))
u2.save_as_mesh(fname('test_mesh_interp_%s_u2.%03d.vtk'
% (field_name, ia)))
return True
def prepare_cylindrical_transform(coors, origin, mode='axes'):
"""
Prepare matrices for transforming tensors into cylindrical coordinates with
the axis 'z' in a given origin.
Parameters
----------
coors : array
The Cartesian coordinates.
origin : array of length 3
The origin.
mode : 'axes' or 'data'
In 'axes' (default) mode the matrix transforms data to different
coordinate system, while in 'data' mode the matrix transforms
the data in the same coordinate system and is transpose of the
matrix in the 'axes' mode.
Returns
-------
mtx : array
The array of transformation matrices for each coordinate in `coors`.
"""
assert_(mode in ['axes', 'data'])
x, y = coors[:,0] - origin[0], coors[:,1] - origin[1]
theta = nm.arctan2(y, x)
if mode == 'data':
theta = -theta
mtx = nm.zeros((coors.shape[0], 3, 3), dtype=nm.float64)
for ii, th in enumerate(theta):
mtx[ii] = make_axis_rotation_matrix([0.0, 0.0, 1.0], th)
return mtx
def __init__(self, anchor, normal, bounds):
Struct.__init__(self, anchor=nm.array(anchor, dtype=nm.float64),
bounds=nm.asarray(bounds, dtype=nm.float64))
self.normal = nm.asarray(normal, dtype=nm.float64)
norm = nm.linalg.norm
self.normal /= norm(self.normal)
e3 = [0.0, 0.0, 1.0]
dd = nm.dot(e3, self.normal)
rot_angle = nm.arccos(dd)
if nm.abs(rot_angle) < 1e-14:
mtx = nm.eye(3, dtype=nm.float64)
bounds2d = self.bounds[:, :2]
else:
rot_axis = nm.cross([0.0, 0.0, 1.0], self.normal)
mtx = la.make_axis_rotation_matrix(rot_axis, rot_angle)
mm = la.insert_strided_axis(mtx, 0, self.bounds.shape[0])
rbounds = la.dot_sequences(mm, self.bounds)
bounds2d = rbounds[:, :2]
assert_(nm.allclose(nm.dot(mtx, self.normal), e3,
rtol=0.0, atol=1e-12))
self.adotn = nm.dot(self.anchor, self.normal)
self.rot_angle = rot_angle
self.mtx = mtx
self.bounds2d = bounds2d
def prepare_cylindrical_transform(coors, origin, mode='axes'):
"""
Prepare matrices for transforming tensors into cylindrical coordinates with
the axis 'z' in a given origin.
Parameters
----------
coors : array
The Cartesian coordinates.
origin : array of length 3
The origin.
mode : 'axes' or 'data'
In 'axes' (default) mode the matrix transforms data to different
coordinate system, while in 'data' mode the matrix transforms
the data in the same coordinate system and is transpose of the
matrix in the 'axes' mode.
Returns
-------
mtx : array
The array of transformation matrices for each coordinate in `coors`.
"""
assert_(mode in ['axes', 'data'])
x, y = coors[:, 0] - origin[0], coors[:, 1] - origin[1]
theta = nm.arctan2(y, x)
if mode == 'data':
theta = -theta
mtx = nm.zeros((coors.shape[0], 3, 3), dtype=nm.float64)
for ii, th in enumerate(theta):
mtx[ii] = make_axis_rotation_matrix([0.0, 0.0, 1.0], th)
return mtx
def prepare_cylindrical_transform(coors, origin):
"""
Prepare matrices for transforming tensors into cylindrical coordinates with
the axis 'z' in a given origin.
Parameters
----------
coors : array
The Cartesian coordinates.
origin : array of length 3
The origin.
Returns
-------
mtx : array
The array of transformation matrices for each coordinate in `coors`.
"""
x, y = coors[:,0] - origin[0], coors[:,1] - origin[1]
theta = nm.arctan2(y, x)
mtx = nm.zeros((coors.shape[0], 3, 3), dtype=nm.float64)
for ii, th in enumerate(theta):
mtx[ii] = make_axis_rotation_matrix([0.0, 0.0, 1.0], th)
return mtx
def get_points(self, refine_flag=None):
"""
Get the probe points.
Returns
-------
pars : array_like
The independent coordinate of the probe.
points : array_like
The probe points, parametrized by pars.
"""
# Vector of angles.
if self.is_refined:
return self.pars, self.points
if refine_flag is None:
pars = nm.linspace(0.0, 2.0 * nm.pi, self.n_point + 1)[:-1]
else:
pars = Probe.refine_pars(self.pars,
refine_flag,
cyclic_val=2.0 * nm.pi)
self.n_point = pars.shape[0]
self.pars = pars
# Create the points in xy plane, centered at the origin.
x = self.radius * nm.cos(pars[:, None])
y = self.radius * nm.sin(pars[:, None])
if len(self.centre) == 3:
z = nm.zeros((self.n_point, 1), dtype=nm.float64)
points = nm.c_[x, y, z]
# Rotate to satisfy the normal, shift to the centre.
n1 = nm.array([0.0, 0.0, 1.0], dtype=nm.float64)
axis = nm.cross(n1, self.normal)
angle = nm.arccos(nm.dot(n1, self.normal))
if nla.norm(axis) < 0.1:
# n1 == self.normal
rot_mtx = nm.eye(3, dtype=nm.float64)
else:
rot_mtx = make_axis_rotation_matrix(axis, angle)
points = nm.dot(points, rot_mtx)
else:
points = nm.c_[x, y]
points += self.centre
self.points = points
return pars, points
def get_points(self, refine_flag=None):
"""
Get the probe points.
Returns
-------
pars : array_like
The independent coordinate of the probe.
points : array_like
The probe points, parametrized by pars.
"""
# Vector of angles.
if self.is_refined:
return self.pars, self.points
if refine_flag is None:
pars = nm.linspace(0.0, 2.0*nm.pi, self.n_point + 1)[:-1]
else:
pars = Probe.refine_pars(self.pars, refine_flag,
cyclic_val=2.0 * nm.pi)
self.n_point = pars.shape[0]
self.pars = pars
# Create the points in xy plane, centered at the origin.
x = self.radius * nm.cos(pars[:,None])
y = self.radius * nm.sin(pars[:,None])
if self.mesh.dim == 3:
z = nm.zeros((self.n_point, 1), dtype=nm.float64)
points = nm.c_[x, y, z]
# Rotate to satisfy the normal, shift to the centre.
n1 = nm.array([0.0, 0.0, 1.0], dtype=nm.float64)
axis = nm.cross(n1, self.normal)
angle = nm.arccos(nm.dot(n1, self.normal))
if nla.norm(axis) < 0.1:
# n1 == self.normal
rot_mtx = nm.eye(3, dtype=nm.float64)
else:
rot_mtx = make_axis_rotation_matrix(axis, angle)
points = nm.dot(points, rot_mtx)
else:
points = nm.c_[x, y]
points += self.centre
self.points = points
return pars, points
def make_mesh(dims, shape, transform=None):
"""
Generate a 2D rectangle mesh in 3D space, and optionally apply a coordinate
transform.
"""
_mesh = gen_block_mesh(dims, shape, [0, 0], name='shell10x', verbose=False)
coors = nm.c_[_mesh.coors, nm.zeros(_mesh.n_nod, dtype=nm.float64)]
coors = nm.ascontiguousarray(coors)
conns = [_mesh.get_conn(_mesh.descs[0])]
mesh = Mesh.from_data(_mesh.name, coors, _mesh.cmesh.vertex_groups, conns,
[_mesh.cmesh.cell_groups], _mesh.descs)
if transform == 'bend':
bbox = mesh.get_bounding_box()
x0, x1 = bbox[:, 0]
angles = 0.5 * nm.pi * (coors[:, 0] - x0) / (x1 - x0)
mtx = make_axis_rotation_matrix([0, -1, 0], angles[:, None, None])
coors = mesh.coors.copy()
coors[:, 0] = 0
coors[:, 2] = (x1 - x0)
mesh.coors[:] = transform_data(coors, mtx=mtx)
mesh.coors[:, 0] -= 0.5 * (x1 - x0)
elif transform == 'twist':
bbox = mesh.get_bounding_box()
x0, x1 = bbox[:, 0]
angles = 0.5 * nm.pi * (coors[:, 0] - x0) / (x1 - x0)
mtx = make_axis_rotation_matrix([-1, 0, 0], angles[:, None, None])
mesh.coors[:] = transform_data(mesh.coors, mtx=mtx)
return mesh
def make_mesh(dims, shape, transform=None):
"""
Generate a 2D rectangle mesh in 3D space, and optionally apply a coordinate
transform.
"""
_mesh = gen_block_mesh(dims, shape, [0, 0], name='shell10x', verbose=False)
coors = nm.c_[_mesh.coors, nm.zeros(_mesh.n_nod, dtype=nm.float64)]
coors = nm.ascontiguousarray(coors)
conns = [_mesh.get_conn(_mesh.descs[0])]
mesh = Mesh.from_data(_mesh.name, coors, _mesh.cmesh.vertex_groups, conns,
[_mesh.cmesh.cell_groups], _mesh.descs)
if transform == 'bend':
bbox = mesh.get_bounding_box()
x0, x1 = bbox[:, 0]
angles = 0.5 * nm.pi * (coors[:, 0] - x0) / (x1 - x0)
mtx = make_axis_rotation_matrix([0, -1, 0], angles[:, None, None])
coors = mesh.coors.copy()
coors[:, 0] = 0
coors[:, 2] = (x1 - x0)
mesh.coors[:] = transform_data(coors, mtx=mtx)
mesh.coors[:, 0] -= 0.5 * (x1 - x0)
elif transform == 'twist':
bbox = mesh.get_bounding_box()
x0, x1 = bbox[:, 0]
angles = 0.5 * nm.pi * (coors[:, 0] - x0) / (x1 - x0)
mtx = make_axis_rotation_matrix([-1, 0, 0], angles[:, None, None])
mesh.coors[:] = transform_data(mesh.coors, mtx=mtx)
return mesh
def test_interpolation(self):
from sfepy import data_dir
from sfepy.fem import Mesh
from sfepy.linalg import make_axis_rotation_matrix
fname = in_dir(self.options.out_dir)
meshes = {
'tp' : Mesh('original mesh', data_dir + '/meshes/3d/block.mesh'),
'si' : Mesh('original mesh', data_dir + '/meshes/3d/cylinder.mesh'),
}
datas = {}
for key, mesh in meshes.iteritems():
bbox = mesh.get_bounding_box()
nx = bbox[1,0] - bbox[0,0]
centre = 0.5 * bbox.sum(axis=0)
mesh.coors -= centre
data = nm.sin(4.0 * nm.pi * mesh.coors[:,0:1] / nx)
datas['scalar_' + key] = data
data = nm.zeros_like(mesh.coors)
data[:,0] = 0.05 * nx * nm.sin(4.0 * nm.pi * mesh.coors[:,0] / nx)
data[:,2] = 0.05 * nx * nm.cos(4.0 * nm.pi * mesh.coors[:,0] / nx)
datas['vector_' + key] = data
for field_name in ['scalar_si', 'vector_si', 'scalar_tp', 'vector_tp']:
m1 = meshes[field_name[-2:]]
for ia, angle in enumerate(nm.linspace(0.0, nm.pi, 11)):
self.report('%s: %d. angle: %f' % (field_name, ia, angle))
shift = [0.0, 0.0, 0.0]
mtx = make_axis_rotation_matrix([0, 1, 0], angle)
m2 = m1.copy('rotated mesh')
m2.transform_coors(mtx)
data = datas[field_name]
u1, u2 = do_interpolation(m2, m1, data, field_name)
if ia == 0:
u1.save_as_mesh(fname('test_mesh_interp_%s_u1.vtk'
% field_name))
u2.save_as_mesh(fname('test_mesh_interp_%s_u2.%03d.vtk'
% (field_name, ia)))
return True
def add_circle_probe(self, name, centre, normal, radius, n_point):
"""
Create the ray (line) probe - VTK object.
Parameters
----------
name : str
The probe name.
centre : array
The coordinates of the circle center point.
normal : array
The normal vector perpendicular to the circle plane.
radius : float
The radius of the circle.
n_point : int
The number of probe points.
"""
pars = nm.linspace(0.0, 2.0*nm.pi, n_point + 1)[:-1]
# Create the points in xy plane, centered at the origin.
x = radius * nm.cos(pars[:,None])
y = radius * nm.sin(pars[:,None])
if len(centre) == 3:
z = nm.zeros((n_point, 1), dtype=nm.float64)
points = nm.c_[x, y, z]
# Rotate to satisfy the normal, shift to the centre.
n1 = nm.array([0.0, 0.0, 1.0], dtype=nm.float64)
axis = nm.cross(n1, normal)
angle = nm.arccos(nm.dot(n1, normal))
if nm.linalg.norm(axis) < 0.1:
# n1 == self.normal
rot_mtx = nm.eye(3, dtype=nm.float64)
else:
rot_mtx = make_axis_rotation_matrix(axis, angle)
points = nm.dot(points, rot_mtx)
else:
points = nm.c_[x, y]
points += centre
circle = self.new_vtk_polyline(points, closed=True)
self.probes[name] = (circle, pars)
self.probes_png[name] = False
def add_circle_probe(self, name, centre, normal, radius, n_point):
"""
Create the ray (line) probe - VTK object.
Parameters
----------
name : str
The probe name.
centre : array
The coordinates of the circle center point.
normal : array
The normal vector perpendicular to the circle plane.
radius : float
The radius of the circle.
n_point : int
The number of probe points.
"""
pars = nm.linspace(0.0, 2.0*nm.pi, n_point + 1)[:-1]
# Create the points in xy plane, centered at the origin.
x = radius * nm.cos(pars[:,None])
y = radius * nm.sin(pars[:,None])
if len(centre) == 3:
z = nm.zeros((n_point, 1), dtype=nm.float64)
points = nm.c_[x, y, z]
# Rotate to satisfy the normal, shift to the centre.
n1 = nm.array([0.0, 0.0, 1.0], dtype=nm.float64)
axis = nm.cross(n1, normal)
angle = nm.arccos(nm.dot(n1, normal))
if nm.linalg.norm(axis) < 0.1:
# n1 == self.normal
rot_mtx = nm.eye(3, dtype=nm.float64)
else:
rot_mtx = make_axis_rotation_matrix(axis, angle)
points = nm.dot(points, rot_mtx)
else:
points = nm.c_[x, y]
points += centre
circle = self.new_vtk_polyline(points, closed=True)
self.probes[name] = (circle, pars)
self.probes_png[name] = False
def plot_faces(ax, gel, radius, n_point, show=False):
"""
Plot faces of a 3D geometry element as numbered oriented arcs. An arc
centre corresponds to the first node of a face. It points from the first
edge towards the last edge of the face.
"""
dim = gel.dim
ax = _get_axes(ax, dim)
if dim < 3: return ax
for ii, face in enumerate(gel.faces):
cc = gel.coors[face]
t1 = cc[1, :] - cc[0, :]
t2 = cc[-1, :] - cc[0, :]
n = nm.cross(t1, t2)
nt1 = nm.linalg.norm(t1)
nt2 = nm.linalg.norm(t2)
angle = nm.arccos(nm.dot(t1, t2) / (nt1 * nt2))
da = angle / (n_point - 1)
mtx = make_axis_rotation_matrix(n, da)
rt = cc[0] + radius * t1 / nt1
coors = [rt]
for ip in range(n_point - 1):
rt = nm.dot(mtx.T, (rt - cc[0])) + cc[0]
coors.append(rt)
coors = nm.array(coors, dtype=nm.float64)
centre = coors.sum(axis=0) / coors.shape[0]
draw_arrow(ax, coors, length=0.3*radius, linewidth=3, color='r')
if dim == 3:
cx, cy, cz = centre
ax.text(cx, cy, cz, ii,
color='r', fontsize=10, weight='light')
else:
cx, cy = centre
ax.text(cx, cy, ii,
color='r', fontsize=10, weight='light')
return ax
def plot_faces(ax, gel, radius, n_point, show=False):
"""
Plot faces of a 3D geometry element as numbered oriented arcs. An arc
centre corresponds to the first node of a face. It points from the first
edge towards the last edge of the face.
"""
dim = gel.dim
ax = _get_axes(ax, dim)
if dim < 3: return ax
for ii, face in enumerate(gel.faces):
cc = gel.coors[face]
t1 = cc[1, :] - cc[0, :]
t2 = cc[-1, :] - cc[0, :]
n = nm.cross(t1, t2)
nt1 = nm.linalg.norm(t1)
nt2 = nm.linalg.norm(t2)
angle = nm.arccos(nm.dot(t1, t2) / (nt1 * nt2))
da = angle / (n_point - 1)
mtx = make_axis_rotation_matrix(n, da)
rt = cc[0] + radius * t1 / nt1
coors = [rt]
for ip in range(n_point - 1):
rt = nm.dot(mtx.T, (rt - cc[0])) + cc[0]
coors.append(rt)
coors = nm.array(coors, dtype=nm.float64)
centre = coors.sum(axis=0) / coors.shape[0]
draw_arrow(ax, coors, length=0.3 * radius, linewidth=3, color='r')
if dim == 3:
cx, cy, cz = centre
ax.text(cx, cy, cz, ii, color='r', fontsize=10, weight='light')
else:
cx, cy = centre
ax.text(cx, cy, ii, color='r', fontsize=10, weight='light')
return ax