def get_points(self):
"""
All points in the block.
"""
for axis, num in ordered_iteritems(self.n_slice):
am = self._axis_map[axis]
shape = np.array((self.resolution[0], self.resolution[1], num))
pb = np.zeros((3,), dtype=np.object)
for ii in range(3):
pb[am[ii]] = np.linspace(0, self.dims[ii], shape[ii])
if num > 1:
delta = pb[am[2]][1] - pb[am[2]][0]
else:
delta = 0.0
x1, x2 = np.meshgrid(pb[am[0]], pb[am[1]])
x1 = x1.ravel()
x2 = x2.ravel()
points = np.empty((x1.shape[0], 3), dtype=np.float64)
points[:,am[0]] = x1
points[:,am[1]] = x2
yield pb, points, delta, num, axis, am
def set_centre(self, centre):
"""
Set the objects's centre and update its description matrix in
homogenous coordinates. Also update the intersector.
"""
self.centre = np.array(centre, dtype=np.float64)
self.mtx_hc = self._get_matrix_hc()
self.intersector.set_data(mtx_hc=self.mtx_hc, centre=self.centre)
def get_circumscribed_ellipsoid(self):
"""
Return a circumscribed ellipsoid of the cylinder.
"""
semiaxes = np.array(3 * [np.sqrt(2.0) * self.radius], dtype=np.float64)
semiaxes[2] *= self.length_to_width
mtx = np.diag(1.0 / (semiaxes**2))
return mtx
def set_centre(self, centre):
"""
Set the objects's centre and update its description matrix in
homogenous coordinates. Also update the intersector.
"""
self.centre = np.array(centre, dtype=np.float64)
self.mtx_hc = self._get_matrix_hc()
self.intersector.set_data(mtx_hc=self.mtx_hc, centre=self.centre)
def __init__(self, dims=None, units=None, resolution=None,
n_object=None, n_slice=None):
Object.__init__(self, name='box',
dims=np.array(dims, dtype=np.float64),
units=units, resolution=resolution,
n_object=n_object, n_slice=n_slice)
if not isinstance(self.n_slice, dict):
self.n_slice = {'z' : int(self.n_slice)}
self.init_trait('volume', np.prod(self.dims))
self._axis_map = {'x' : [1, 2, 0], 'y' : [2, 0, 1], 'z' : [0, 1, 2]}
def contains(self, points):
"""
Point x in cylinder. Works for array of points.
Parameters
----------
points : (n_point, 3) array
The points to be tested for inclusion.
"""
points = np.array(points, ndmin=2, dtype=np.float64)
x = points.T - self.centre[:,np.newaxis]
aux = np.dot(self.rot_mtx, x)
r = np.sqrt(aux[0,:]**2 + aux[1,:]**2)
mask = (np.abs(aux[2,:]) <= (0.5 * self.height)) & (r <= self.radius)
return mask
def contains(self, points):
"""
Point x in ellipsoid A <=> x^T A x <= 1.
Works for array of points.
Parameters:
points : (n_point, 3) array
"""
points = np.array(points, ndmin=2, dtype=np.float64)
x = points.T - self.centre[:, np.newaxis]
aux = np.sum(x * np.dot(self.mtx, x), axis=0)
mask = np.where(aux <= 1.0, True, False)
## x2 = np.r_[points.T, np.ones((1,points.shape[0]))]
## aux2 = np.sum(x2 * np.dot(self.mtx_hc, x2), axis = 0)
## mask2 = np.where(aux2 <= 0.0, True, False)
## print np.alltrue(mask == mask2)
return mask
def contains(self, points):
"""
Point x in ellipsoid A <=> x^T A x <= 1.
Works for array of points.
Parameters:
points : (n_point, 3) array
"""
points = np.array(points, ndmin=2, dtype=np.float64)
x = points.T - self.centre[:,np.newaxis]
aux = np.sum(x * np.dot(self.mtx, x), axis = 0)
mask = np.where(aux <= 1.0, True, False)
## x2 = np.r_[points.T, np.ones((1,points.shape[0]))]
## aux2 = np.sum(x2 * np.dot(self.mtx_hc, x2), axis = 0)
## mask2 = np.where(aux2 <= 0.0, True, False)
## print np.alltrue(mask == mask2)
return mask
def __init__(self, semiaxes):
"""
Parameters:
semiaxes : (float, float, float)
The semiaxes a, b, c of the ellipsoid.
"""
self.semiaxes = np.array(semiaxes, dtype=np.float64)
self.mtx0 = np.diag(1.0 / (self.semiaxes**2))
im = self.semiaxes.argmax()
self.direction0 = np.eye(3, dtype=np.float64)[im]
self.volume = 4.0 / 3.0 * np.pi * np.prod(self.semiaxes)
self.surface = self.compute_approximate_surface()
self.length = self.semiaxes[im]
self.is_placed = False
self.intersection_counters = {}
self.intersector = EllipsoidIntersector()
def __init__(self, semiaxes):
"""
Parameters:
semiaxes : (float, float, float)
The semiaxes a, b, c of the ellipsoid.
"""
self.semiaxes = np.array(semiaxes, dtype=np.float64)
self.mtx0 = np.diag(1.0 / (self.semiaxes**2))
im = self.semiaxes.argmax()
self.direction0 = np.eye(3, dtype=np.float64)[im]
self.volume = 4.0 / 3.0 * np.pi * np.prod(self.semiaxes)
self.surface = self.compute_approximate_surface()
self.length = self.semiaxes[im]
self.is_placed = False
self.intersection_counters = {}
self.intersector = EllipsoidIntersector()
def __init__(self, radius, height):
"""
Parameters
----------
radius : float
The radius of the cylinder.
height : float
The height of the cylinder.
"""
self.radius = radius
self.height = height
self.length_to_width = 0.5 * height / radius
self.mtx0 = self.get_circumscribed_ellipsoid()
self.direction0 = np.array([0.0, 0.0, 1.0], dtype=np.float64)
self.volume = height * np.pi * (radius**2)
self.surface = 2.0 * np.pi * radius * height
self.length = self.height
self.is_placed = False
self.intersection_counters = {}
self.intersector = EllipsoidIntersector()
def set_centre(self, centre):
"""
Set the intersector's centre.
"""
self.centre = np.array(centre, dtype=np.float64)
def set_centre(self, centre):
"""
Set the intersector's centre.
"""
self.centre = np.array(centre, dtype=np.float64)
