def __init__(self,
center,
A,
B,
C,
e0,
tilt,
fields=None,
ds=None,
field_parameters=None,
data_source=None):
YTSelectionContainer3D.__init__(self, center, ds, field_parameters,
data_source)
# make sure the magnitudes of semi-major axes are in order
if A < B or B < C:
raise YTEllipsoidOrdering(ds, A, B, C)
# make sure the smallest side is not smaller than dx
self._A = self.ds.quan(A, 'code_length')
self._B = self.ds.quan(B, 'code_length')
self._C = self.ds.quan(C, 'code_length')
if self._C < self.index.get_smallest_dx():
raise YTSphereTooSmall(self.ds, self._C,
self.index.get_smallest_dx())
self._e0 = e0 = e0 / (e0**2.0).sum()**0.5
self._tilt = tilt
# find the t1 angle needed to rotate about z axis to align e0 to x
t1 = np.arctan(e0[1] / e0[0])
# rotate e0 by -t1
RZ = get_rotation_matrix(t1, (0, 0, 1)).transpose()
r1 = (e0 * RZ).sum(axis=1)
# find the t2 angle needed to rotate about y axis to align e0 to x
t2 = np.arctan(-r1[2] / r1[0])
"""
calculate the original e1
given the tilt about the x axis when e0 was aligned
to x after t1, t2 rotations about z, y
"""
RX = get_rotation_matrix(-tilt, (1, 0, 0)).transpose()
RY = get_rotation_matrix(-t2, (0, 1, 0)).transpose()
RZ = get_rotation_matrix(-t1, (0, 0, 1)).transpose()
e1 = ((0, 1, 0) * RX).sum(axis=1)
e1 = (e1 * RY).sum(axis=1)
e1 = (e1 * RZ).sum(axis=1)
e2 = np.cross(e0, e1)
self._e1 = e1
self._e2 = e2
self.set_field_parameter('A', A)
self.set_field_parameter('B', B)
self.set_field_parameter('C', C)
self.set_field_parameter('e0', e0)
self.set_field_parameter('e1', e1)
self.set_field_parameter('e2', e2)
def _get_sampler_params(self, camera, render_source):
px = np.linspace(-np.pi, np.pi, camera.resolution[0],
endpoint=True)[:, None]
py = np.linspace(-np.pi / 2.0,
np.pi / 2.0,
camera.resolution[1],
endpoint=True)[None, :]
vectors = np.zeros((camera.resolution[0], camera.resolution[1], 3),
dtype="float64",
order="C")
vectors[:, :, 0] = np.cos(px) * np.cos(py)
vectors[:, :, 1] = np.sin(px) * np.cos(py)
vectors[:, :, 2] = np.sin(py)
# The maximum possible length of ray
max_length = unorm(camera.position - camera._domain_center
) + 0.5 * unorm(camera._domain_width)
# Rescale the ray to be long enough to cover the entire domain
vectors = vectors * max_length
positions = np.tile(camera.position, camera.resolution[0] *
camera.resolution[1]).reshape(
camera.resolution[0], camera.resolution[1], 3)
R1 = get_rotation_matrix(0.5 * np.pi, [1, 0, 0])
R2 = get_rotation_matrix(0.5 * np.pi, [0, 0, 1])
uv = np.dot(R1, camera.unit_vectors)
uv = np.dot(R2, uv)
vectors.reshape((camera.resolution[0] * camera.resolution[1], 3))
vectors = np.dot(vectors, uv)
vectors.reshape((camera.resolution[0], camera.resolution[1], 3))
if render_source.zbuffer is not None:
image = render_source.zbuffer.rgba
else:
image = self.new_image(camera)
dummy = np.ones(3, dtype="float64")
image.shape = (camera.resolution[0], camera.resolution[1], 4)
vectors.shape = (camera.resolution[0], camera.resolution[1], 3)
positions.shape = (camera.resolution[0], camera.resolution[1], 3)
sampler_params = dict(
vp_pos=positions,
vp_dir=vectors,
center=self.back_center,
bounds=(0.0, 1.0, 0.0, 1.0),
x_vec=dummy,
y_vec=dummy,
width=np.zeros(3, dtype="float64"),
image=image,
lens_type="spherical",
)
return sampler_params
def rotate(self, theta, rot_vector=None, rot_center=None):
r"""Rotate by a given angle
Rotate the view. If `rot_vector` is None, rotation will occur
around the `north_vector`.
Parameters
----------
theta : float, in radians
Angle (in radians) by which to rotate the view.
rot_vector : array_like, optional
Specify the rotation vector around which rotation will
occur. Defaults to None, which sets rotation around
`north_vector`
rot_center : array_like, optional
Specify the center around which rotation will occur. Defaults
to None, which sets rotation around the original camera position
(i.e. the camera position does not change)
Examples
--------
>>> import yt
>>> import numpy as np
>>> from yt.visualization.volume_rendering.api import Scene
>>> sc = Scene()
>>> cam = sc.add_camera()
>>> # rotate the camera by pi / 4 radians:
>>> cam.rotate(np.pi/4.0)
>>> # rotate the camera about the y-axis instead of cam.north_vector:
>>> cam.rotate(np.pi/4.0, np.array([0.0, 1.0, 0.0]))
>>> # rotate the camera about the origin instead of its own position:
>>> cam.rotate(np.pi/4.0, rot_center=np.array([0.0, 0.0, 0.0]))
"""
rotate_all = rot_vector is not None
if rot_vector is None:
rot_vector = self.north_vector
if rot_center is None:
rot_center = self._position
rot_vector = ensure_numpy_array(rot_vector)
rot_vector = rot_vector/np.linalg.norm(rot_vector)
new_position = self._position - rot_center
R = get_rotation_matrix(theta, rot_vector)
new_position = np.dot(R, new_position) + rot_center
if (new_position == self._position).all():
normal_vector = self.unit_vectors[2]
else:
normal_vector = rot_center - new_position
normal_vector = normal_vector/np.sqrt((normal_vector**2).sum())
if rotate_all:
self.switch_view(
normal_vector=np.dot(R, normal_vector),
north_vector=np.dot(R, self.unit_vectors[1]))
else:
self.switch_view(normal_vector=np.dot(R, normal_vector))
if (new_position != self._position).any(): self.set_position(new_position)
def _get_positions_vectors(self, camera, disparity):
single_resolution_x = int(np.floor(camera.resolution[0]) / 2)
east_vec = camera.unit_vectors[0]
north_vec = camera.unit_vectors[1]
normal_vec = camera.unit_vectors[2]
angle_disparity = - np.arctan2(disparity.in_units(camera.width.units),
camera.width[2])
R = get_rotation_matrix(angle_disparity, north_vec)
east_vec_rot = np.dot(R, east_vec)
normal_vec_rot = np.dot(R, normal_vec)
px = np.mat(np.linspace(-.5, .5, single_resolution_x))
py = np.mat(np.linspace(-.5, .5, camera.resolution[1]))
sample_x = camera.width[0] * np.array(east_vec_rot.reshape(3, 1) * px)
sample_x = sample_x.transpose()
sample_y = camera.width[1] * np.array(north_vec.reshape(3, 1) * py)
sample_y = sample_y.transpose()
vectors = np.zeros((single_resolution_x, camera.resolution[1], 3),
dtype='float64', order='C')
sample_x = np.repeat(sample_x.reshape(single_resolution_x, 1, 3),
camera.resolution[1], axis=1)
sample_y = np.repeat(sample_y.reshape(1, camera.resolution[1], 3),
single_resolution_x, axis=0)
normal_vecs = np.tile(
normal_vec_rot, single_resolution_x * camera.resolution[1])
normal_vecs = normal_vecs.reshape(
single_resolution_x, camera.resolution[1], 3)
east_vecs = np.tile(
east_vec_rot, single_resolution_x * camera.resolution[1])
east_vecs = east_vecs.reshape(
single_resolution_x, camera.resolution[1], 3)
# The maximum possible length of ray
max_length = (unorm(camera.position - camera._domain_center)
+ 0.5 * unorm(camera._domain_width)
+ np.abs(self.disparity))
# Rescale the ray to be long enough to cover the entire domain
vectors = (sample_x + sample_y + normal_vecs * camera.width[2]) * \
(max_length / camera.width[2])
positions = np.tile(
camera.position, single_resolution_x * camera.resolution[1])
positions = positions.reshape(
single_resolution_x, camera.resolution[1], 3)
# Here the east_vecs is non-rotated one
positions = positions + east_vecs * disparity
mylog.debug(positions)
mylog.debug(vectors)
return vectors, positions
def __init__(self, center, A, B, C, e0, tilt, fields=None,
ds=None, field_parameters=None, data_source=None):
YTSelectionContainer3D.__init__(self, center, ds,
field_parameters, data_source)
# make sure the magnitudes of semi-major axes are in order
if A<B or B<C:
raise YTEllipsoidOrdering(ds, A, B, C)
# make sure the smallest side is not smaller than dx
self._A = self.ds.quan(A, 'code_length')
self._B = self.ds.quan(B, 'code_length')
self._C = self.ds.quan(C, 'code_length')
if self._C < self.index.get_smallest_dx():
raise YTSphereTooSmall(self.ds, self._C, self.index.get_smallest_dx())
self._e0 = e0 = e0 / (e0**2.0).sum()**0.5
self._tilt = tilt
# find the t1 angle needed to rotate about z axis to align e0 to x
t1 = np.arctan(e0[1] / e0[0])
# rotate e0 by -t1
RZ = get_rotation_matrix(t1, (0,0,1)).transpose()
r1 = (e0 * RZ).sum(axis = 1)
# find the t2 angle needed to rotate about y axis to align e0 to x
t2 = np.arctan(-r1[2] / r1[0])
"""
calculate the original e1
given the tilt about the x axis when e0 was aligned
to x after t1, t2 rotations about z, y
"""
RX = get_rotation_matrix(-tilt, (1, 0, 0)).transpose()
RY = get_rotation_matrix(-t2, (0, 1, 0)).transpose()
RZ = get_rotation_matrix(-t1, (0, 0, 1)).transpose()
e1 = ((0, 1, 0) * RX).sum(axis=1)
e1 = (e1 * RY).sum(axis=1)
e1 = (e1 * RZ).sum(axis=1)
e2 = np.cross(e0, e1)
self._e1 = e1
self._e2 = e2
self.set_field_parameter('A', A)
self.set_field_parameter('B', B)
self.set_field_parameter('C', C)
self.set_field_parameter('e0', e0)
self.set_field_parameter('e1', e1)
self.set_field_parameter('e2', e2)
def _get_px_py_dz(self, camera, pos, res, disparity):
res0_h = np.floor(res[0]) / 2
east_vec = camera.unit_vectors[0]
north_vec = camera.unit_vectors[1]
normal_vec = camera.unit_vectors[2]
angle_disparity = -np.arctan2(disparity.d, camera.width[2].d)
R = get_rotation_matrix(angle_disparity, north_vec)
east_vec_rot = np.dot(R, east_vec)
normal_vec_rot = np.dot(R, normal_vec)
camera_position_shift = camera.position + east_vec * disparity
camera_position_shift = camera_position_shift.in_units('code_length').d
width = camera.width.in_units('code_length').d
sight_vector = pos - camera_position_shift
pos1 = sight_vector
for i in range(0, sight_vector.shape[0]):
sight_vector_norm = np.sqrt(
np.dot(sight_vector[i], sight_vector[i]))
sight_vector[i] = sight_vector[i] / sight_vector_norm
sight_center = camera_position_shift + camera.width[2] * normal_vec_rot
for i in range(0, sight_vector.shape[0]):
sight_angle_cos = np.dot(sight_vector[i], normal_vec_rot)
# clip sight_angle_cos since floating point noise might
# cause it go outside the domain of arccos
sight_angle_cos = np.clip(sight_angle_cos, -1.0, 1.0)
if np.arccos(sight_angle_cos) < 0.5 * np.pi:
sight_length = width[2] / sight_angle_cos
else:
# If the corner is on the backwards, then we put it outside of
# the image It can not be simply removed because it may connect
# to other corner within the image, which produces visible
# domain boundary line
sight_length = np.sqrt(width[0]**2 + width[1]**2)
sight_length = sight_length / np.sqrt(1 - sight_angle_cos**2)
pos1[i] = camera_position_shift + sight_length * sight_vector[i]
dx = np.dot(pos1 - sight_center, east_vec_rot)
dy = np.dot(pos1 - sight_center, north_vec)
dz = np.dot(pos - camera_position_shift, normal_vec_rot)
# Transpose into image coords.
if disparity > 0:
px = (res0_h * 0.5 + res0_h / camera.width[0].d * dx).astype('int')
else:
px = (res0_h * 1.5 + res0_h / camera.width[0].d * dx).astype('int')
py = (res[1] * 0.5 + res[1] / camera.width[1].d * dy).astype('int')
return px, py, dz
def _get_sampler_params(self, camera, render_source):
if self.disparity is None:
self.disparity = camera.width[0] / 1000.
single_resolution_y = int(np.floor(camera.resolution[1]) / 2)
px = np.linspace(-np.pi, np.pi, camera.resolution[0],
endpoint=True)[:, None]
py = np.linspace(-np.pi / 2.,
np.pi / 2.,
single_resolution_y,
endpoint=True)[None, :]
vectors = np.zeros((camera.resolution[0], single_resolution_y, 3),
dtype='float64',
order='C')
vectors[:, :, 0] = np.cos(px) * np.cos(py)
vectors[:, :, 1] = np.sin(px) * np.cos(py)
vectors[:, :, 2] = np.sin(py)
# The maximum possible length of ray
max_length = (unorm(camera.position - camera._domain_center) +
0.5 * unorm(camera._domain_width) +
np.abs(self.disparity))
# Rescale the ray to be long enough to cover the entire domain
vectors = vectors * max_length
R1 = get_rotation_matrix(0.5 * np.pi, [1, 0, 0])
R2 = get_rotation_matrix(0.5 * np.pi, [0, 0, 1])
uv = np.dot(R1, camera.unit_vectors)
uv = np.dot(R2, uv)
vectors.reshape((camera.resolution[0] * single_resolution_y, 3))
vectors = np.dot(vectors, uv)
vectors.reshape((camera.resolution[0], single_resolution_y, 3))
vectors2 = np.zeros((camera.resolution[0], single_resolution_y, 3),
dtype='float64',
order='C')
vectors2[:, :, 0] = -np.sin(px) * np.ones((1, single_resolution_y))
vectors2[:, :, 1] = np.cos(px) * np.ones((1, single_resolution_y))
vectors2[:, :, 2] = 0
vectors2.reshape((camera.resolution[0] * single_resolution_y, 3))
vectors2 = np.dot(vectors2, uv)
vectors2.reshape((camera.resolution[0], single_resolution_y, 3))
positions = np.tile(camera.position,
camera.resolution[0] * single_resolution_y)
positions = positions.reshape(camera.resolution[0],
single_resolution_y, 3)
# The left and right are switched here since VR is in LHS.
positions_left = positions + vectors2 * self.disparity
positions_right = positions + vectors2 * (-self.disparity)
if render_source.zbuffer is not None:
image = render_source.zbuffer.rgba
else:
image = self.new_image(camera)
dummy = np.ones(3, dtype='float64')
vectors_comb = uhstack([vectors, vectors])
positions_comb = uhstack([positions_left, positions_right])
image.shape = (camera.resolution[0], camera.resolution[1], 4)
vectors_comb.shape = (camera.resolution[0], camera.resolution[1], 3)
positions_comb.shape = (camera.resolution[0], camera.resolution[1], 3)
sampler_params = dict(vp_pos=positions_comb,
vp_dir=vectors_comb,
center=self.back_center,
bounds=(0.0, 1.0, 0.0, 1.0),
x_vec=dummy,
y_vec=dummy,
width=np.zeros(3, dtype="float64"),
image=image,
lens_type="stereo-spherical")
return sampler_params
def _get_ellipsoid_parameters_basic(self):
np.seterr(all="ignore")
# check if there are 4 particles to form an ellipsoid
# neglecting to check if the 4 particles in the same plane,
# that is almost certainly never to occur,
# will deal with it later if it ever comes up
if np.size(self["particle_position_x"]) < 4:
mylog.warning("Too few particles for ellipsoid parameters.")
return (0, 0, 0, 0, 0, 0, 0)
# Calculate the parameters that describe the ellipsoid of
# the particles that constitute the halo. This function returns
# all the parameters except for the center of mass.
com = self.center_of_mass()
position = [
self["particle_position_x"],
self["particle_position_y"],
self["particle_position_z"],
]
# Locate the furthest particle from com, its vector length and index
DW = np.array([self.gridsize[0], self.gridsize[1], self.gridsize[2]])
position = [position[0] - com[0], position[1] - com[1], position[2] - com[2]]
# different cases of particles being on other side of boundary
for axis in range(np.size(DW)):
cases = np.array(
[position[axis], position[axis] + DW[axis], position[axis] - DW[axis]]
)
# pick out the smallest absolute distance from com
position[axis] = np.choose(np.abs(cases).argmin(axis=0), cases)
# find the furthest particle's index
r = np.sqrt(position[0] ** 2 + position[1] ** 2 + position[2] ** 2)
A_index = r.argmax()
mag_A = r.max()
# designate the A vector
A_vector = (position[0][A_index], position[1][A_index], position[2][A_index])
# designate the e0 unit vector
e0_vector = A_vector / mag_A
# locate the tB particle position by finding the max B
e0_vector_copy = np.empty((np.size(position[0]), 3), dtype="float64")
for i in range(3):
e0_vector_copy[:, i] = e0_vector[i]
rr = np.array(
[position[0], position[1], position[2]]
).T # Similar to tB_vector in old code.
tC_vector = np.cross(e0_vector_copy, rr)
te2 = tC_vector.copy()
for dim in range(3):
te2[:, dim] *= np.sum(tC_vector**2.0, axis=1) ** (-0.5)
te1 = np.cross(te2, e0_vector_copy)
length = np.abs(
-np.sum(rr * te1, axis=1)
* (1.0 - np.sum(rr * e0_vector_copy, axis=1) ** 2.0 * mag_A**-2.0)
** (-0.5)
)
# This problem apparently happens sometimes, that the NaNs are turned
# into infs, which messes up the nanargmax below.
length[length == np.inf] = 0.0
tB_index = np.nanargmax(length) # ignores NaNs created above.
mag_B = length[tB_index]
e1_vector = te1[tB_index]
e2_vector = te2[tB_index]
temp_e0 = rr.copy()
temp_e1 = rr.copy()
temp_e2 = rr.copy()
for dim in range(3):
temp_e0[:, dim] = e0_vector[dim]
temp_e1[:, dim] = e1_vector[dim]
temp_e2[:, dim] = e2_vector[dim]
length = np.abs(
np.sum(rr * temp_e2, axis=1)
* (
1
- np.sum(rr * temp_e0, axis=1) ** 2.0 * mag_A**-2.0
- np.sum(rr * temp_e1, axis=1) ** 2.0 * mag_B**-2.0
)
** (-0.5)
)
length[length == np.inf] = 0.0
tC_index = np.nanargmax(length)
mag_C = length[tC_index]
# tilt is calculated from the rotation about x axis
# needed to align e1 vector with the y axis
# after e0 is aligned with x axis
# find the t1 angle needed to rotate about z axis to align e0 onto x-z plane
t1 = np.arctan(-e0_vector[1] / e0_vector[0])
RZ = get_rotation_matrix(t1, (0, 0, 1))
r1 = np.dot(RZ, e0_vector)
# find the t2 angle needed to rotate about y axis to align e0 to x
t2 = np.arctan(r1[2] / r1[0])
RY = get_rotation_matrix(t2, (0, 1, 0))
r2 = np.dot(RY, np.dot(RZ, e1_vector))
# find the tilt angle needed to rotate about x axis to align e1 to y and e2 to z
tilt = np.arctan(-r2[2] / r2[1])
return (mag_A, mag_B, mag_C, e0_vector[0], e0_vector[1], e0_vector[2], tilt)